Mercurial > repos > galaxyp > psm_to_sam

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