fix shed.yml lint warnings

data_managers/data_manager_gatk_picard_index_builder/.shed.yml

@@ -5,4 +5,5 @@ long_description:
 name: data_manager_gatk_picard_index_builder
 owner: devteam
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder
 type: unrestricted

data_managers/data_manager_packaged_annotation_data/.shed.yml

@@ -9,4 +9,5 @@ long_description: |
 name: data_manager_packaged_annotation_data
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_packaged_annotation_data
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_packaged_annotation_data
 type: unrestricted

data_managers/data_manager_pangolin_data/.shed.yml

@@ -7,4 +7,5 @@ long_description: |
 name: data_manager_pangolin_data
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data
 type: unrestricted

data_managers/data_manager_star_index_builder/.shed.yml

@@ -8,4 +8,5 @@ long_description: |
 name: data_manager_star_index_builder
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder
 type: unrestricted

tools/allegro/.shed.yml

@@ -1,6 +1,7 @@
 name: allegro
 owner: iuc
 description: Linkage and haplotype analysis from deCODE
+long_description: A fast linkage and haplotype analysis utility making use of MTBDD to reduce complexity.
 homepage_url: http://www.decode.com/software/
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/
 categories:

tools/art/.shed.yml

@@ -4,10 +4,9 @@ name: art
 description: Simulator for Illumina, 454, and SOLiD sequencing data
 long_description: |
     Sequencing data simulation tools
-
-    http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
 categories:
     - Sequence Analysis
     - Data Source
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/art
+homepage_url: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
 type: unrestricted

tools/b2btools/.shed.yml

@@ -5,6 +5,7 @@ long_description: |
     Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting them
     to biological events and improving our understanding of the way proteins work.
 homepage_url: https://bio2byte.be
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools
 type: unrestricted
 categories:
     - Computational chemistry

tools/barrnap/.shed.yml

@@ -4,5 +4,7 @@ description: Contains the Barrnap tool for finding ribosomal RNAs in FASTA seque
 long_description: |
   Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. Barrnap now supports Archaea, Eukaryota and Mitochondria.
 name: barrnap
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap
+homepage_url: https://github.com/tseemann/barrnap
 owner: iuc
-type: unrestricted
+type: unrestricted

tools/blastxml_to_gapped_gff3/.shed.yml

@@ -7,4 +7,5 @@ long_description: |
 name: blastxml_to_gapped_gff3
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3
 type: unrestricted

tools/charts/.shed.yml

@@ -6,6 +6,7 @@ long_description: |
     The pre-processing is done by this tool. Noteworthy, many chart types like e.g. Bar diagrams and Scatterplots, do not require data pre-processing.
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/
 type: unrestricted
 name: charts
 description:  Enables advanced visualization options in Galaxy Charts

tools/collection_column_join/.shed.yml

@@ -6,3 +6,4 @@ long_description: |
 name: collection_column_join
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join

tools/collection_element_identifiers/.shed.yml

@@ -4,3 +4,4 @@ description: Extract element identifiers of a collection
 name: collection_element_identifiers
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers

tools/column_order_header_sort/.shed.yml

@@ -6,3 +6,4 @@ long_description: |
 name: column_order_header_sort
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort

tools/column_remove_by_header/.shed.yml

@@ -6,3 +6,4 @@ long_description: |
 name: column_remove_by_header
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header

tools/compress_file/.shed.yml

@@ -6,4 +6,5 @@ long_description: |
 name: compress_file
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file
 type: unrestricted

tools/deg_annotate/.shed.yml

@@ -8,4 +8,5 @@ long_description: |
 name: deg_annotate
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate
 type: unrestricted

tools/flair/.shed.yml

@@ -1,6 +1,10 @@
 name: flair
 owner: iuc
 description: FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.
+long_description: |
+    FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform 
+    definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been 
+    used for nanopore cDNA, native RNA, and PacBio sequencing reads.
 homepage_url: https://github.com/BrooksLabUCSC/flair
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair
 type: unrestricted
@@ -12,4 +16,8 @@ auto_tool_repositories:
 suite:
   name: "suite_flair"
   description: FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.
+  long_description: |
+    FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform 
+    definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been 
+    used for nanopore cDNA, native RNA, and PacBio sequencing reads.
   type: repository_suite_definition

tools/genehunter_modscore/.shed.yml

@@ -1,7 +1,8 @@
 name: genehunter_modscore
 owner: iuc
 description: Maximised LOD score pedigree analysis utility
-homepage_url: https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html
+long_description: A MOD-score analysis in which parametric LOD scores are maximized over the parameters of the trait model
+homepage_url: https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/
 categories:
   - Variant Analysis

tools/gvcftools/.shed.yml

@@ -4,6 +4,10 @@ owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools
 homepage_url: https://github.com/sequencing/gvcftools
 type: unrestricted
+long_description: |
+    gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.
+    gVCF are VCF 4.1 files which follow a set of conventions for representing all sites
+    in the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
   description_template: "Wrapper for ngsutils tool: {{ tool_name }}"

tools/hicstuff/.shed.yml

@@ -1,13 +1,15 @@
+owner: iuc
 categories:
 - Sequence Analysis
 homepage_url: https://github.com/koszullab/hicstuff
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff
+long_description: A toolkit to generate and manipulate Hi-C matrices
+type: unrestricted
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
   description_template: "{{ tool_name }} (from the hicstuff tool suite)"
 suite:
     name: suite_hicstuff
     description: A toolkit to generate and manipulate Hi-C matrices
     long_description: A toolkit to generate and manipulate Hi-C matrices
-owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff
-type: unrestricted
+

tools/hivclustering/.shed.yml

@@ -1,6 +1,7 @@
 name: hivclustering
 owner: iuc
 description: Infers transmission networks from pairwise distances inferred by tn93
+long_description: Infers transmission networks from pairwise distances inferred by tn93
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/
 homepage_url: https://pypi.org/project/hivclustering/
 type: unrestricted

tools/intermine_galaxy_exchange/.shed.yml

@@ -6,3 +6,4 @@ long_description: |
 name: intermine_galaxy_exchange
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange
+homepage_url: https://github.com/intermine

tools/join_files_by_id/.shed.yml

@@ -9,4 +9,5 @@ long_description: |
 categories:
     - Text Manipulation
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id
 type: unrestricted

tools/king/.shed.yml

@@ -1,7 +1,8 @@
 name: king
 owner: iuc
 description: Kinship-based INference for Gwas
+long_description: Kinship-based INference for Gwas (KING) is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study
 homepage_url: http://people.virginia.edu/~wc9c/KING/
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/
 categories:
-  - Variant Analysis
+  - Variant Analysis

tools/merlin/.shed.yml

@@ -1,7 +1,8 @@
 name: merlin
 owner: iuc
 description: Pedigree Analysis package
+long_description: MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around
 homepage_url: http://csg.sph.umich.edu/abecasis/Merlin/
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/
 categories:
-  - Variant Analysis
+  - Variant Analysis

tools/metagenomeseq/.shed.yml

@@ -6,4 +6,5 @@ long_description: |
 name: metagenomeseq_normalization
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
+homepage_url: https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html
 type: unrestricted

tools/multigps/.shed.yml

@@ -1,13 +1,14 @@
 name: multigps
 owner: iuc
 description: Analyzes collections of multi-condition ChIP-seq data.
-homepage_url: http://mahonylab.org/software/multigps/
 long_description: |
   Contains a tool that runs MultiGPS, a framework for analyzing collections of multi-condition ChIP-seq
   datasets and characterizing differential binding events between conditions.  MultiGPS encourages consistency
   in the reported binding event locations across conditions and provides accurate estimation of ChIP enrichment
   levels at each event.  MultiGPS loads all data to memory, so you will need a lot of available memory if you
   are running analysis over many conditions or large datasets.
+homepage_url: http://mahonylab.org/software/multigps/
+remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps"
 type: unrestricted
 categories:
 - ChIP-seq

tools/packaged_annotation_loader/.shed.yml

@@ -9,4 +9,5 @@ long_description: |
 name: packaged_annotation_loader
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader
 type: unrestricted

tools/pilon/.shed.yml

@@ -5,8 +5,8 @@ long_description: |
    Pilon is a software tool which can be used to:
        * Automatically improve draft assemblies
        * Find variation among strains, including large event detection
-   https://github.com/broadinstitute/pilon/wiki
 name: pilon
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon
+homepage_url: https://github.com/broadinstitute/pilon/wiki
 type: unrestricted

tools/plink/.shed.yml

@@ -1,6 +1,7 @@
 name: plink
 owner: iuc
-description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
+description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
+long_description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
 homepage_url: https://www.cog-genomics.org/plink
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink
 type: unrestricted

tools/prinseq/.shed.yml

@@ -2,6 +2,7 @@ categories:
  - Fastq Manipulation
  - Metagenomics
 description: PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets
+long_description: PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets
 homepage_url: http://prinseq.sourceforge.net/manual.html
 name: prinseq
 owner: iuc 

tools/progressivemauve/.shed.yml

@@ -20,4 +20,5 @@ long_description: |
 name: progressivemauve
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve
+homepage_url: http://darlinglab.org/mauve/user-guide/progressivemauve.html
 type: unrestricted

tools/quickmerge/.shed.yml

@@ -6,3 +6,8 @@ categories:
   - Assembly
 type: unrestricted
 description: Merge long-read and hybrid assemblies to increase contiguity
+long_description: |
+    The program uses complementary information from genomes assembled with long reads in 
+    order to improve contiguity, and works with assemblies derived from both Pacific 
+    Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies 
+    made by combining long reads and Illumina short reads. 

tools/sbml2sbol/.shed.yml

@@ -2,6 +2,7 @@ categories:
 - Synthetic Biology
 description: Convert SBML to SBOL format
 homepage_url: https://github.com/neilswainston/SbmlToSbol
+remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol"
 long_description: 'This tool takes a pathway model (encoded in SBML) as input and returns a collection of placeholders for the subsequent design of the synthetic DNA that is required to encode the enzymes defined in the pathway model (encoded in SBOL).'
 name: sbml2sbol
 owner: iuc

tools/snpfreqplot/.shed.yml

@@ -1,7 +1,8 @@
 name: snpfreqplot
 owner: iuc
-description: Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data
-homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/
+description: A plotting app to visualise the SNPs across a region
+long_description: Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data
+homepage_url: https://github.com/BrownfieldPlantLab/SNPFreqPlot
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/
 categories:
   - Variant Analysis

tools/star_fusion/.shed.yml

@@ -12,4 +12,5 @@ long_description: |
 name: star_fusion
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion
+homepage_url: https://github.com/STAR-Fusion/STAR-Fusion
 type: unrestricted

tools/strelka/.shed.yml

@@ -2,6 +2,19 @@ name: strelka
 owner: iuc
 remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka"
 homepage_url: "https://github.com/Illumina/strelka/"
+long_description: |
+    Strelka2 is a fast and accurate small variant caller optimized
+    for analysis of germline variation in small cohorts and somatic
+    variation in tumor/normal sample pairs. The germline caller employs an
+    efficient tiered haplotype model to improve accuracy and provide read-backed
+    phasing, adaptively selecting between assembly and a faster alignment-based
+    haplotyping approach at each variant locus. The germline caller also analyzes
+    input sequencing data using a mixture-model indel error estimation method to
+    improve robustness to indel noise. The somatic calling model improves on the
+    original Strelka method for liquid and late-stage tumor analysis by accounting
+    for possible tumor cell contamination in the normal sample. A final empirical
+    variant re-scoring step using random forest models trained on various call
+    quality features has been added to both callers to further improve precision.
 categories:
 - "Variant Analysis"
 auto_tool_repositories:
@@ -22,4 +35,4 @@ suite:
     original Strelka method for liquid and late-stage tumor analysis by accounting
     for possible tumor cell contamination in the normal sample. A final empirical
     variant re-scoring step using random forest models trained on various call
-    quality features has been added to both callers to further improve precision.
+    quality features has been added to both callers to further improve precision.

tools/structure/.shed.yml

@@ -14,4 +14,5 @@ long_description: |
 name: structure
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
+homepage_url: https://web.stanford.edu/group/pritchardlab/structure.html
 type: unrestricted

tools/structureharvester/.shed.yml

@@ -3,8 +3,9 @@ categories:
 - Variant Analysis
 description: for parsing STRUCTURE outputs and for performing the Evanno method
 long_description: |
-  http://taylor0.biology.ucla.edu/structureHarvester/
+  structureHarvester.py is a Python script capable of extracting all the relevant data from STRUCTURE results files
 name: structureharvester
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester
+homepage_url: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/
 type: unrestricted

tools/swift/.shed.yml

@@ -1,6 +1,10 @@
 name: swiftlink
 owner: iuc
 description: Parallel MCMC Linkage Analysis
+long_description: | 
+    A multipoint parametric linkage analysis tool for large consanguineous pedigrees and is 
+    primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm 
+    based program, i.e. many markers, but larger pedigree
 homepage_url: https://github.com/ajm/swiftlink
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/
 categories:

tools/table_compute/.shed.yml

@@ -1,10 +1,11 @@
 categories:
 - Text Manipulation
+description: Perform general-purpose table operations
 long_description: |
   Operations such as; sorting, subselecting, duplicating, expression evaluation, and more.
   These can be performed on the row, column, or element level.
 owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute
 type: unrestricted
 name: table_compute
-description: Perform general-purpose table operations

tools/tasmanian_mismatch/.shed.yml

@@ -3,6 +3,7 @@ description: Analysis of positional mismatches
 long_description: A tool to count and visualize the distribution of positional mismatches from reads of High throughput DNA sequencing experiments
 owner: iuc
 type: unrestricted
-remote_repository_url: https://github.com/nebiolabs/tasmanian-mismatch
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch
+homepage_url: https://github.com/nebiolabs/tasmanian-mismatch
 categories:
 - Sequence Analysis