Merge pull request #1377 from mvdbeek/update_collection_operation_too…

…l_list

Update collection operation tool list

planemo/galaxy/distro_tools.py

@@ -20,7 +20,6 @@
     "gff_filter_by_attribute": "filters/gff/gff_filter_by_attribute.xml",
     "gtf2bedgraph": "filters/gtf2bedgraph.xml",
     "ChangeCase": "filters/changeCase.xml",
-    "__FLATTEN__": "${model_tools_path}/flatten_collection.xml",
     "wiggle2simple1": "filters/wiggle_to_simple.xml",
     "GeneBed_Maf_Fasta2": "maf/genebed_maf_to_fasta.xml",
     "trimmer": "filters/trimmer.xml",
@@ -32,17 +31,30 @@
     "barchart_gnuplot": "plotting/bar_chart.xml",
     "microbial_import1": "data_source/microbial_import.xml",
     "axt_to_concat_fasta": "filters/axt_to_concat_fasta.xml",
-    "__FILTER_FROM_FILE__": "${model_tools_path}/filter_from_file.xml",
     "Interval2Maf_pairwise1": "maf/interval2maf_pairwise.xml",
     "Show beginning1": "filters/headWrapper.xml",
     "axt_to_lav_1": "filters/axt_to_lav.xml",
     "modmine": "data_source/modmine.xml",
-    "__EXPORT_HISTORY__": "${model_tools_path}/imp_exp/exp_history_to_archive.xml",
     "MAF_Thread_For_Species1": "maf/maf_thread_for_species.xml",
     "vcf_to_maf_customtrack1": "maf/vcf_to_maf_customtrack.xml",
     "MAF_To_BED1": "maf/maf_to_bed.xml",
     "__DATA_FETCH__": "${model_tools_path}/data_fetch.xml",
     "__IMPORT_HISTORY__": "${model_tools_path}/imp_exp/imp_history_from_archive.xml",
+    "__EXPORT_HISTORY__": "${model_tools_path}/imp_exp/exp_history_to_archive.xml",
+    "__UNZIP_COLLECTION__": "${model_tools_path}/unzip_collection.xml",
+    "__ZIP_COLLECTION__": "${model_tools_path}/zip_collection.xml",
+    "__FILTER_FAILED_DATASETS__": "${model_tools_path}/filter_failed_collection.xml",
+    "__FILTER_EMPTY_DATASETS__": "${model_tools_path}/filter_empty_collection.xml",
+    "__FLATTEN__": "${model_tools_path}/flatten_collection.xml",
+    "__SORTLIST__": "${model_tools_path}/sort_collection_list.xml",
+    "__MERGE_COLLECTION__": "${model_tools_path}/merge_collection.xml",
+    "__RELABEL_FROM_FILE__": "${model_tools_path}/relabel_from_file.xml",
+    "__FILTER_FROM_FILE__": "${model_tools_path}/filter_from_file.xml",
+    "__TAG_FROM_FILE__": "${model_tools_path}/tag_collection_from_file.xml",
+    "__APPLY_RULES__": "${model_tools_path}/apply_rules.xml",
+    "__BUILD_LIST__": ["${model_tools_path}/build_list.xml", "${model_tools_path}/build_list_1.2.0.xml"],
+    "__EXTRACT_DATASET__": "${model_tools_path}/extract_dataset.xml",
+    "__DUPLICATE_FILE_TO_COLLECTION__": "${model_tools_path}/duplicate_file_to_collection.xml",
     "biomart": "data_source/biomart.xml",
     "Sff_extractor": "filters/sff_extractor.xml",
     "secure_hash_message_digest": "filters/secure_hash_message_digest.xml",
@@ -71,31 +83,25 @@
     "gtf_filter_by_attribute_values_list": "filters/gff/gtf_filter_by_attribute_values_list.xml",
     "Summary_Statistics1": "stats/gsummary.xml",
     "qual_stats_boxplot": "plotting/boxplot.xml",
-    "cat1": ["filters/catWrapper.xml", "filters/catWrapper2.xml"],
+    "cat1": "filters/catWrapper.xml",
     "maf_by_block_number1": "maf/maf_by_block_number.xml",
     "Grep1": "filters/grep.xml",
     "eupathdb": "data_source/eupathdb.xml",
-    "__RELABEL_FROM_FILE__": "${model_tools_path}/relabel_from_file.xml",
-    "__ZIP_COLLECTION__": "${model_tools_path}/zip_collection.xml",
     "lav_to_bed1": "filters/lav_to_bed.xml",
     "comp1": "filters/compare.xml",
     "bed_to_bigBed": "filters/bed_to_bigbed.xml",
     "liftOver1": "extract/liftOver_wrapper.xml",
     "bed2gff1": "filters/bed2gff.xml",
-    "__MERGE_COLLECTION__": "${model_tools_path}/merge_collection.xml",
     "gramenemart": "data_source/gramene_mart.xml",
     "hbvar": "data_source/hbvar.xml",
     "yeastmine": "data_source/yeastmine.xml",
     "Filter1": "stats/filtering.xml",
     "flymine": "data_source/flymine.xml",
     "wormbase_test": "data_source/wormbase_test.xml",
-    "__FILTER_FAILED_DATASETS__": "${model_tools_path}/filter_failed_collection.xml",
     "Extract genomic DNA 1": "extract/extract_genomic_dna.xml",
     "Remove beginning1": "filters/remove_beginning.xml",
     "flymine_test": "data_source/flymine_test.xml",
     "axt_to_fasta": "filters/axt_to_fasta.xml",
     "addValue": "filters/fixedValueColumn.xml",
-    "__TAG_FROM_FILE__": "${model_tools_path}/tag_collection_from_file.xml",
     "param_value_from_file": "expression_tools/parse_values_from_file.xml",
-    "__APPLY_RULES__": "${model_tools_path}/apply_rules.xml",
 }