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comparison PSM2SAM.xml @ 0:90ecb65017a0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
author galaxyp
date Wed, 17 May 2017 20:23:27 -0400
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children 3192cb6a88f6
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-1:000000000000 0:90ecb65017a0
1 <tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2">
2 <description>Generate SAM files from PSMs.</description>
3 <requirements>
4 <requirement type="package" version="3.3.1">r-base</requirement>
5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
9 <requirement type="package" version="1.11.1">r-devtools</requirement>
10 <requirement type="package" version="3.98_1.4">r-xml</requirement>
11 <requirement type="package" version="0.10.11">r-rmysql</requirement>
12 <requirement type="package" version="1.0.2">r-testthat</requirement>
13 <requirement type="package" version="0.1.0">r-getoptlong</requirement>
14 <requirement type="package" version="1.1.2">r-stringi</requirement>
15 <requirement type="package" version="1.1.0">r-stringr</requirement>
16 <requirement type="package" version="1.10.0">r-data.table</requirement>
17 <requirement type="package" version="0.4_10">r-sqldf</requirement>
18 <requirement type="package" version="0.6_6">r-gsubfn</requirement>
19 <requirement type="package" version="2.3_47">r-chron</requirement>
20 <requirement type="package" version="0.3.10">r-proto</requirement>
21 <requirement type="package" version="1.8.4">r-plyr</requirement>
22 <requirement type="package" version="1.1_0">r-fastmatch</requirement>
23 <requirement type="package" version="0.1.0">r-ahocorasicktrie</requirement>
24 </requirements>
25 <stdio>
26 <exit_code range="1:" level="fatal" description="Job Failed" />
27 </stdio>
28 <command><![CDATA[
29 Rscript --vanilla '$__tool_directory__/PSM2SAM.R'
30
31 #if str($input.input_type) == "idpicker":
32 --idpDB="$input.input_file"
33 --searchEngineScore="$input.scoreColumn"
34 #else if str($input.input_type) == "peptideshaker":
35 --peptideShakerPsmReport="$input.input_file"
36 #else if str($input.input_type) == "pepxmltab":
37 --pepXmlTab="$input.input_file"
38 --searchEngineScore="$input.scoreColumn"
39 #end if
40
41 --bam="$bam_file"
42
43 #if str($variantAnnotation_file) != 'None':
44 --variantAnnotation="$variantAnnotation_file"
45 #end if
46
47 #if str($genome_annotation.source) == "history":
48 --exon_anno="$genome_annotation.exonAnno"
49 --proteinseq="$genome_annotation.proteinSeq"
50 --procodingseq="$genome_annotation.proCodingSeq"
51 #else:
52 #set index_path = $genome_annotation.builtin.fields.path
53 --exon_anno="$index_path/exon_anno.RData"
54 --proteinseq="$index_path/proseq.RData"
55 --procodingseq="$index_path/procodingseq.RData"
56 #end if
57 2>&1
58 ]]>
59 </command>
60 <inputs>
61 <conditional name="input">
62 <param name="input_type" 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">
63 <option value="idpicker">IDPicker idpDB</option>
64 <option value="peptideshaker">PeptideShaker PSM report</option>
65 <option value="pepxmltab">PepXmlTab</option>
66 </param>
67 <when value="idpicker">
68 <param name="input_file" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
69 <validator type="empty_field" message="This field is required."/>
70 </param>
71 <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">
72 <validator type="empty_field" message="This field is required."/>
73 </param>
74 </when>
75 <when value="peptideshaker">
76 <param name="input_file" type="data" format="tabular" help="A PeptideShaker PSM report to convert to SAM" label="Input PSMs">
77 <validator type="empty_field" message="This field is required."/>
78 </param>
79 </when>
80 <when value="pepxmltab">
81 <param name="input_file" type="data" format="tabular" help="A pepXmlTab file to convert to SAM" label="Input PSMs">
82 <validator type="empty_field" message="This field is required."/>
83 </param>
84 <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. &quot;mvh&quot;)" size="60" label="Score Name">
85 <validator type="empty_field" message="This field is required."/>
86 </param>
87 </when>
88 </conditional>
89 <conditional name="genome_annotation">
90 <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">
91 <option value="builtin">Use a built-in genome annotation</option>
92 <option value="history">Use annotation from your history</option>
93 </param>
94 <when value="builtin">
95 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
96 <options from_data_table="customProDB">
97 <filter type="sort_by" column="2"/>
98 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
99 </options>
100 </param>
101 </when>
102 <when value="history">
103 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
104 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
105 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
106 </when>
107 </conditional>
108 <param name="bam_file" type="data" format="bam,sam" help="A SAM or BAM file to extract headers from (i.e. sequence metadata from reference genome)" label="SAM/BAM Headers">
109 <validator type="empty_field" message="This field is required."/>
110 </param>
111 <param name="variantAnnotation_file" type="data" format="RData" help="A variant annotation .RData file from customProDB." label="Variant Annotation" optional="true" />
112 </inputs>
113 <outputs>
114 <data format="sam" name="output_sam" from_work_dir="output.sam" label="${input.input_file.name.rsplit('.',1)[0]}.sam"/>
115 </outputs>
116 <tests>
117 <test>
118 <param name="input_type" value="idpicker" />
119 <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" />
120 <param name="scoreColumn" value="Myrimatch:MVH" />
121 <param name="source" value="history" />
122 <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" />
123 <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" />
124 <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" />
125 <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" />
126 <param name="variantAnnotation_file" value="hg19/hg19_variant_annotation.RData" dbkey="hg19" />
127 <output name="output" file="idpicker_hg19_with_variants.sam" />
128 </test>
129 <test>
130 <param name="input_type" value="idpicker" />
131 <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" />
132 <param name="scoreColumn" value="Myrimatch:MVH" />
133 <param name="source" value="history" />
134 <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" />
135 <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" />
136 <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" />
137 <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" />
138 <output name="output" file="idpicker_hg19_no_variants.sam" />
139 </test>
140 <!--<test>
141 <param name="input_type" value="pepxmltab" />
142 <param name="input_file" value="passedPSM.tab" dbkey="hg19" />
143 <param name="scoreColumn" value="Myrimatch:MVH" />
144 <param name="source" value="history" />
145 <param name="exonAnno" value="gencode/exon_anno.RData" dbkey="hg19" />
146 <param name="proteinSeq" value="gencode/proseq.RData" dbkey="hg19" />
147 <param name="proCodingSeq" value="gencode/procodingseq.RData" dbkey="hg19" />
148 <output name="output" file="pepXmlTab_gencode.sam" />
149 </test>-->
150 <test>
151 <param name="input_type" value="peptideshaker" />
152 <param name="input_file" value="mm10/test.psm-report" dbkey="mm9" />
153 <param name="source" value="history" />
154 <param name="exonAnno" value="mm10/exon_anno.RData" dbkey="mm9" />
155 <param name="proteinSeq" value="mm10/proseq.RData" dbkey="mm9" />
156 <param name="proCodingSeq" value="mm10/procodingseq.RData" dbkey="mm9" />
157 <param name="bam_file" value="mm10/Sample_Mouse_pro-B_total.whole_exp.bam" dbkey="mm9" />
158 <param name="variantAnnotation_file" value="mm10/mm10_variant_annotation.RData" dbkey="mm9" />
159 <output name="output" file="peptideshaker_mm10.sam" />
160 </test>
161 </tests>
162 <help>
163 **Description**
164
165 Generate SAM files from confident peptide-spectrum-matches (PSMs).
166 </help>
167 </tool>