Mercurial > repos > galaxyp > psm_to_sam

comparison PSM2SAM.xml @ 2:e1bb35f6ca28 draft

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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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1:34f9e847dd4e 2:e1bb35f6ca28
32 <validator type="empty_field" message="This field is required."/> 32 <validator type="empty_field" message="This field is required."/>
33 </param> 33 </param>
34 <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. &quot;MyriMatch:mvh&quot;)" size="60" label="Score Name"> 34 <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. &quot;MyriMatch:mvh&quot;)" size="60" label="Score Name">
35 <validator type="empty_field" message="This field is required."/> 35 <validator type="empty_field" message="This field is required."/>
36 </param> 36 </param>
37 <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences"> 37 <conditional name="optionalUserInput">
38 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> 38 <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" />
39 <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" /> 39 <when value="true">
40 <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" /> 40 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
41 <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" /> 41 <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" />
42 </section> 42 <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" />
43 <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" />
44 </when>
45 <when value="false">
46 </when>
47 </conditional>
43 </inputs> 48 </inputs>
44 <outputs> 49 <outputs>
45 <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/> 50 <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>
46 </outputs> 51 </outputs>
47 <!--<tests> 52 <!--<tests>