Mercurial > repos > galaxyp > psm_to_sam

annotate PSM2SAM.xml @ 2:e1bb35f6ca28 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 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Thu, 14 Jan 2016 18:13:18 -0500
parents 34f9e847dd4e
children ce09f1a1bbad
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>
1
34f9e847dd4e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents: 0
diff changeset
3 <stdio>
34f9e847dd4e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents: 0
diff changeset
4 <exit_code range="1:" level="fatal" description="Job Failed" />
34f9e847dd4e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
galaxyp
parents: 0
diff changeset
5 </stdio>
0
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
6 <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
7 #if str($input).strip() != "":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
8 --passedPSM="$input"
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
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($scoreColumn).strip() != "":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
11 --XScolumn="$scoreColumn"
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
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($optionalUserInput.exonAnno).strip() != "None":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
14 --exon_anno="$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
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($optionalUserInput.proteinSeq).strip() != "None":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
17 --proteinseq="$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
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($optionalUserInput.proCodingSeq).strip() != "None":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
20 --procodingseq="$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
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($optionalUserInput.header).strip() != "None":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
23 --header="$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
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 #if str($output).strip() != "":
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
26 --OutputFile="$output"
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
27 #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
28
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
29 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
30 <inputs>
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="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
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 <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
35 <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
36 </param>
2
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
37 <conditional name="optionalUserInput">
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
38 <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" />
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
39 <when value="true">
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
40 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
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" />
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
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" />
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
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" />
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
44 </when>
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
45 <when value="false">
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
46 </when>
e1bb35f6ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 1
diff changeset
47 </conditional>
0
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
48 </inputs>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
49 <outputs>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
50 <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
51 </outputs>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
52 <!--<tests>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
53 <test>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
54 <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
55 <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
56 <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
57 </test>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
58 <test>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
59 <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
60 <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
61 <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
62 </test>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
63 </tests>-->
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
64 <help>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
65 **Description**
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
66
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
67 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
68 </help>
c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
galaxyp
parents:
diff changeset
69 </tool>