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lint fixes
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@bgruening
bgruening committed Feb 25, 2024
1 parent cd041b4 commit c40c139
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Showing 4 changed files with 64 additions and 80 deletions.
2 changes: 1 addition & 1 deletion tools/meme/dreme.xml
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<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>- Discriminative Regular Expression Motif Elicitation</description>
<macros>
<import>macros.xml</import>
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40 changes: 12 additions & 28 deletions tools/meme/fimo.xml
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@@ -1,11 +1,11 @@
<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>- Scan a set of sequences for motifs</description>
<xrefs>
<xref type="bio.tools">meme_fimo</xref>
</xrefs>
<macros>
<import>macros.xml</import>
</macros>
<xrefs>
<xref type="bio.tools">meme_fimo</xref>
</xrefs>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
Expand Down Expand Up @@ -82,12 +82,8 @@ fimo
</param>
<when value="basic"/>
<when value="advanced">
<param name="thresh" type="float" value="1e-4" argument="--thresh"
label="Output threshold for displaying search results"
help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
<param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh"
type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False"
help="Default: apply set threshold on p-values"/>
<param argument="--thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
<param argument="--qv-thresh" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" label="Apply output threshold to q-values?" help="Default: apply set threshold on p-values"/>
<conditional name="bgfile_type">
<param name="bgfile_type_selector" type="select" label="Background model selection">
<option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
Expand All @@ -102,12 +98,8 @@ fimo
<param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/>
</when>
</conditional>
<param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand"
type="boolean" truevalue="--max-strand" falsevalue="" checked="False"
help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
<param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores"
label="Maximum number of scores that will be stored"
help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
<param argument="--max-strand" type="boolean" truevalue="--max-strand" falsevalue="" checked="False" label="Report best match in case of overlapping matches on both strands?" help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
<param argument="--max-stored-scores" type="integer" value="100000" label="Maximum number of scores that will be stored" help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
<conditional name="motifs_cond">
<param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
<option value="no" selected="true">No</option>
Expand All @@ -123,15 +115,9 @@ fimo
</repeat>
</when>
</conditional>
<param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo"
label="Pseudocount to add to counts in motif matrix"
help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
<param name="no_qvalue" label="Disable q-value calculation?"
type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue"
help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
<param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?"
type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord"
help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
<param argument="--motif-pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
<param argument="--no-qvalue" type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" label="Disable q-value calculation?" help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
<param argument="--parse-genomic-coord" type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" label="Check each sequence header for UCSC-style genomic coordinates?" help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
<conditional name="psp_cond">
<param name="psp_selector" type="select" label="Use position-specific priors?">
<option value="no" selected="true">No</option>
Expand All @@ -142,9 +128,7 @@ fimo
<param name="input_psp" type="data" format="txt" argument="--psp"
label="Select file containing position-specific priors"
help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
<param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha"
label="Alpha parameter for calculating position-specific priors"
help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)"/>
<param argument="--alpha" type="float" min="0" max="1.0" value="1.0" label="Alpha parameter for calculating position-specific priors" help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)"/>
</when>
</conditional>
<conditional name="prior_dist_cond">
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