Mercurial > repos > galaxyp > psm_to_sam
diff PSM2SAM.xml @ 2:e1bb35f6ca28 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
| author | galaxyp |
|---|---|
| date | Thu, 14 Jan 2016 18:13:18 -0500 |
| parents | 34f9e847dd4e |
| children | ce09f1a1bbad |
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--- a/PSM2SAM.xml Thu Nov 12 18:11:28 2015 -0500 +++ b/PSM2SAM.xml Thu Jan 14 18:13:18 2016 -0500 @@ -34,12 +34,17 @@ <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. "MyriMatch:mvh")" size="60" label="Score Name"> <validator type="empty_field" message="This field is required."/> </param> - <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences"> - <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> - <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> - <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> - <param name="header" type="data" format="txt" help="A text file of SAM headers to include in the output file, usually corresponding to the exon and coding sequences used." label="SAM Headers" optional="true" /> - </section> + <conditional name="optionalUserInput"> + <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" /> + <when value="true"> + <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> + <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> + <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> + <param name="header" type="data" format="txt" help="A text file of SAM headers to include in the output file, usually corresponding to the exon and coding sequences used." label="SAM Headers" optional="true" /> + </when> + <when value="false"> + </when> + </conditional> </inputs> <outputs> <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>