Mercurial > repos > galaxyp > psm_to_sam

comparison PSM2SAM.xml @ 0:c506e5dac2bb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
author galaxyp
date Fri, 02 Oct 2015 14:14:15 -0400
parents
children 34f9e847dd4e
comparison
equal deleted inserted replaced
-1:000000000000 0:c506e5dac2bb
1 <tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2">
2 <description>Generate SAM files from PSMs.</description>
3 <command interpreter="Rscript --vanilla">PSM2SAM.R
4 #if str($input).strip() != "":
5 --passedPSM="$input"
6 #end if
7 #if str($scoreColumn).strip() != "":
8 --XScolumn="$scoreColumn"
9 #end if
10 #if str($optionalUserInput.exonAnno).strip() != "None":
11 --exon_anno="$optionalUserInput.exonAnno"
12 #end if
13 #if str($optionalUserInput.proteinSeq).strip() != "None":
14 --proteinseq="$optionalUserInput.proteinSeq"
15 #end if
16 #if str($optionalUserInput.proCodingSeq).strip() != "None":
17 --procodingseq="$optionalUserInput.proCodingSeq"
18 #end if
19 #if str($optionalUserInput.header).strip() != "None":
20 --header="$optionalUserInput.header"
21 #end if
22 #if str($output).strip() != "":
23 --OutputFile="$output"
24 #end if
25
26 2&gt;&amp;1</command>
27 <inputs>
28 <param name="input" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
29 <validator type="empty_field" message="This field is required."/>
30 </param>
31 <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">
32 <validator type="empty_field" message="This field is required."/>
33 </param>
34 <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences">
35 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
36 <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" />
37 <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" />
38 <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" />
39 </section>
40 </inputs>
41 <outputs>
42 <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>
43 </outputs>
44 <!--<tests>
45 <test>
46 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
47 <param name="scoreColumn" value="Myrimatch:MVH" />
48 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
49 </test>
50 <test>
51 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
52 <param name="scoreColumn" value="Myrimatch:MVH" />
53 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
54 </test>
55 </tests>-->
56 <help>
57 **Description**
58
59 Generate SAM files from confident peptide-spectrum-matches (PSMs).
60 </help>
61 </tool>