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comparison PSM2SAM.xml @ 3:ce09f1a1bbad 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, 28 Jan 2016 18:40:54 -0500
parents e1bb35f6ca28
children cd69250e1150
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2:e1bb35f6ca28 3:ce09f1a1bbad
2 <description>Generate SAM files from PSMs.</description> 2 <description>Generate SAM files from PSMs.</description>
3 <stdio> 3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" /> 4 <exit_code range="1:" level="fatal" description="Job Failed" />
5 </stdio> 5 </stdio>
6 <command interpreter="Rscript --vanilla">PSM2SAM.R 6 <command interpreter="Rscript --vanilla">PSM2SAM.R
7 #if str($input).strip() != "": 7
8 --passedPSM="$input" 8 --passedPSM="$input"
9 #end if 9 --XScolumn="$scoreColumn"
10 #if str($scoreColumn).strip() != "": 10 --header="$samHeaders"
11 --XScolumn="$scoreColumn" 11 --OutputFile="$output"
12 #end if 12
13 #if str($optionalUserInput.exonAnno).strip() != "None": 13 #if str($genome_annotation.source) == "history":
14 --exon_anno="$optionalUserInput.exonAnno" 14 --exon_anno="$genome_annotation.exonAnno"
15 #end if 15 --proteinseq="$genome_annotation.proteinSeq"
16 #if str($optionalUserInput.proteinSeq).strip() != "None": 16 --procodingseq="$genome_annotation.proCodingSeq"
17 --proteinseq="$optionalUserInput.proteinSeq" 17 #else:
18 #end if 18 #set index_path = $genome_annotation.builtin.fields.path
19 #if str($optionalUserInput.proCodingSeq).strip() != "None": 19 --exon_anno="$index_path/exon_anno.RData"
20 --procodingseq="$optionalUserInput.proCodingSeq" 20 --proteinseq="$index_path/proseq.RData"
21 #end if 21 --procodingseq="$index_path/procodingseq.RData"
22 #if str($optionalUserInput.header).strip() != "None":
23 --header="$optionalUserInput.header"
24 #end if
25 #if str($output).strip() != "":
26 --OutputFile="$output"
27 #end if 22 #end if
28 23
29 2&gt;&amp;1</command> 24 2&gt;&amp;1</command>
30 <inputs> 25 <inputs>
31 <param name="input" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs"> 26 <param name="input" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
32 <validator type="empty_field" message="This field is required."/> 27 <validator type="empty_field" message="This field is required."/>
33 </param> 28 </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"> 29 <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."/> 30 <validator type="empty_field" message="This field is required."/>
36 </param> 31 </param>
37 <conditional name="optionalUserInput"> 32
38 <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" /> 33 <conditional name="genome_annotation">
39 <when value="true"> 34 <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
40 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> 35 <option value="builtin">Use a built-in genome annotation</option>
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" /> 36 <option value="history">Use annotation from your history</option>
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" /> 37 </param>
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" /> 38 <when value="builtin">
39 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
40 <options from_data_table="customProDB">
41 <filter type="sort_by" column="2"/>
42 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
43 </options>
44 </param>
44 </when> 45 </when>
45 <when value="false"> 46 <when value="history">
47 <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
48 <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
49 <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
46 </when> 50 </when>
47 </conditional> 51 </conditional>
52 <param name="samHeaders" type="data" format="txt" help="A text file of SAM headers extracted from the original SAM/BAM file or reference genome" label="SAM/BAM Headers">
53 <validator type="empty_field" message="This field is required."/>
54 </param>
48 </inputs> 55 </inputs>
49 <outputs> 56 <outputs>
50 <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/> 57 <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>
51 </outputs> 58 </outputs>
52 <!--<tests> 59 <tests>
53 <test> 60 <test>
54 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" /> 61 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB" />
55 <param name="scoreColumn" value="Myrimatch:MVH" /> 62 <param name="scoreColumn" value="Myrimatch:MVH" />
63 <param name="source" value="history" />
64 <param name="exonAnno" value="exon_anno.RData" />
65 <param name="proteinSeq" value="proseq.RData" />
66 <param name="proCodingSeq" value="procodingseq.RData" />
67 <param name="samHeaders" value="header_refseq_hg19.txt" />
56 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" /> 68 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
57 </test> 69 </test>
58 <test> 70 <test>
59 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" /> 71 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB" />
60 <param name="scoreColumn" value="Myrimatch:MVH" /> 72 <param name="scoreColumn" value="Myrimatch:MVH" />
73 <param name="source" value="history" />
74 <param name="exonAnno" value="exon_anno.RData" />
75 <param name="proteinSeq" value="proseq.RData" />
76 <param name="proCodingSeq" value="procodingseq.RData" />
77 <param name="samHeaders" value="header_refseq_hg19.txt" />
61 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" /> 78 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
62 </test> 79 </test>
63 </tests>--> 80 </tests>
64 <help> 81 <help>
65 **Description** 82 **Description**
66 83
67 Generate SAM files from confident peptide-spectrum-matches (PSMs). 84 Generate SAM files from confident peptide-spectrum-matches (PSMs).
68 </help> 85 </help>