Mercurial > repos > galaxyp > psm_to_sam

annotate PSM2SAM.xml @ 2:757ecf27b4a9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 969036a4673f5565185badb0d4fe513a7b784261
author galaxyp
date Mon, 25 Sep 2017 13:23:54 -0400
parents 3192cb6a88f6
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1 <tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2.1">
0
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2 <description>Generate SAM files from PSMs.</description>
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3 <requirements>
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4 <requirement type="package" version="3.3.1">r-base</requirement>
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5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
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6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
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7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
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8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
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9 <requirement type="package" version="1.11.1">r-devtools</requirement>
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10 <requirement type="package" version="3.98_1.4">r-xml</requirement>
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11 <requirement type="package" version="0.10.11">r-rmysql</requirement>
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12 <requirement type="package" version="1.0.2">r-testthat</requirement>
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13 <requirement type="package" version="0.1.0">r-getoptlong</requirement>
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14 <requirement type="package" version="1.1.2">r-stringi</requirement>
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15 <requirement type="package" version="1.1.0">r-stringr</requirement>
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16 <requirement type="package" version="1.10.0">r-data.table</requirement>
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17 <requirement type="package" version="0.4_10">r-sqldf</requirement>
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18 <requirement type="package" version="0.6_6">r-gsubfn</requirement>
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19 <requirement type="package" version="2.3_47">r-chron</requirement>
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20 <requirement type="package" version="0.3_10">r-proto</requirement>
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21 <requirement type="package" version="1.8.4">r-plyr</requirement>
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22 <requirement type="package" version="1.1_0">r-fastmatch</requirement>
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23 <requirement type="package" version="0.1.0">r-ahocorasicktrie</requirement>
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24 </requirements>
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25 <stdio>
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26 <exit_code range="1:" level="fatal" description="Job Failed" />
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27 </stdio>
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28 <command><![CDATA[
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29 Rscript --vanilla '$__tool_directory__/PSM2SAM.R'
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30
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31 #if str($input.input_type) == "idpicker":
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32 --idpDB="$input.input_file"
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33 --searchEngineScore="$input.scoreColumn"
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34 #else if str($input.input_type) == "peptideshaker":
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35 --peptideShakerPsmReport="$input.input_file"
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36 #else if str($input.input_type) == "pepxmltab":
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37 --pepXmlTab="$input.input_file"
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38 --searchEngineScore="$input.scoreColumn"
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39 #end if
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40
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41 --bam="$bam_file"
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42
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43 #if str($variantAnnotation_file) != 'None':
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44 --variantAnnotation="$variantAnnotation_file"
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45 #end if
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46
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47 #if str($genome_annotation.source) == "history":
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48 --exon_anno="$genome_annotation.exonAnno"
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49 --proteinseq="$genome_annotation.proteinSeq"
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50 --procodingseq="$genome_annotation.proCodingSeq"
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51 #else:
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52 #set index_path = $genome_annotation.builtin.fields.path
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53 --exon_anno="$index_path/exon_anno.RData"
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54 --proteinseq="$index_path/proseq.RData"
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55 --procodingseq="$index_path/procodingseq.RData"
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56 #end if
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57 2>&1
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58 ]]>
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59 </command>
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60 <inputs>
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61 <conditional name="input">
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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">
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63 <option value="idpicker">IDPicker idpDB</option>
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64 <option value="peptideshaker">PeptideShaker PSM report</option>
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65 <option value="pepxmltab">PepXmlTab</option>
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66 </param>
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67 <when value="idpicker">
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68 <param name="input_file" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
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69 <validator type="empty_field" message="This field is required."/>
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70 </param>
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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">
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72 <validator type="empty_field" message="This field is required."/>
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73 </param>
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74 </when>
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75 <when value="peptideshaker">
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76 <param name="input_file" type="data" format="tabular" help="A PeptideShaker PSM report to convert to SAM" label="Input PSMs">
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77 <validator type="empty_field" message="This field is required."/>
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78 </param>
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79 </when>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
80 <when value="pepxmltab">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
81 <param name="input_file" type="data" format="tabular" help="A pepXmlTab file to convert to SAM" label="Input PSMs">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
82 <validator type="empty_field" message="This field is required."/>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
83 </param>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
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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">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
85 <validator type="empty_field" message="This field is required."/>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
86 </param>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
87 </when>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
88 </conditional>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
89 <conditional name="genome_annotation">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
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">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
91 <option value="builtin">Use a built-in genome annotation</option>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
92 <option value="history">Use annotation from your history</option>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
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93 </param>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
94 <when value="builtin">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
95 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
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96 <options from_data_table="customProDB">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
97 <filter type="sort_by" column="2"/>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
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98 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
99 </options>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
100 </param>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
101 </when>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
102 <when value="history">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
103 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
104 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
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" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
106 </when>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
107 </conditional>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
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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">
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
109 <validator type="empty_field" message="This field is required."/>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
110 </param>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
111 <param name="variantAnnotation_file" type="data" format="RData" help="A variant annotation .RData file from customProDB." label="Variant Annotation" optional="true" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
112 </inputs>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
113 <outputs>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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114 <data format="sam" name="output_sam" from_work_dir="output.sam" label="${input.input_file.name.rsplit('.',1)[0]}.sam"/>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
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115 </outputs>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
116 <tests>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
117 <test>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
118 <param name="input_type" value="idpicker" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
119 <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
120 <param name="scoreColumn" value="Myrimatch:MVH" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
121 <param name="source" value="history" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
122 <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
123 <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
124 <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
125 <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
126 <param name="variantAnnotation_file" value="hg19/hg19_variant_annotation.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
127 <output name="output" file="idpicker_hg19_with_variants.sam" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
128 </test>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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129 <test>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
130 <param name="input_type" value="idpicker" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
131 <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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132 <param name="scoreColumn" value="Myrimatch:MVH" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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133 <param name="source" value="history" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
134 <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
135 <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
136 <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
137 <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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138 <output name="output" file="idpicker_hg19_no_variants.sam" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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139 </test>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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140 <!--<test>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
141 <param name="input_type" value="pepxmltab" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
142 <param name="input_file" value="passedPSM.tab" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
143 <param name="scoreColumn" value="Myrimatch:MVH" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
144 <param name="source" value="history" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
145 <param name="exonAnno" value="gencode/exon_anno.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
146 <param name="proteinSeq" value="gencode/proseq.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
147 <param name="proCodingSeq" value="gencode/procodingseq.RData" dbkey="hg19" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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148 <output name="output" file="pepXmlTab_gencode.sam" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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149 </test>-->
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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150 <test>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
151 <param name="input_type" value="peptideshaker" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
152 <param name="input_file" value="mm10/test.psm-report" dbkey="mm9" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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153 <param name="source" value="history" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
parents:
diff changeset
154 <param name="exonAnno" value="mm10/exon_anno.RData" dbkey="mm9" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
155 <param name="proteinSeq" value="mm10/proseq.RData" dbkey="mm9" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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diff changeset
156 <param name="proCodingSeq" value="mm10/procodingseq.RData" dbkey="mm9" />
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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157 <param name="bam_file" value="mm10/Sample_Mouse_pro-B_total.whole_exp.bam" dbkey="mm9" />
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158 <param name="variantAnnotation_file" value="mm10/mm10_variant_annotation.RData" dbkey="mm9" />
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159 <output name="output" file="peptideshaker_mm10.sam" />
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160 </test>
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161 </tests>
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162 <help>
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163 **Description**
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164
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165 Generate SAM files from confident peptide-spectrum-matches (PSMs).
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166 </help>
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167 </tool>