Mercurial > repos > galaxyp > psm_to_sam
diff PSM2SAM.xml @ 0:90ecb65017a0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
author | galaxyp |
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date | Wed, 17 May 2017 20:23:27 -0400 |
parents | |
children | 3192cb6a88f6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PSM2SAM.xml Wed May 17 20:23:27 2017 -0400 @@ -0,0 +1,167 @@ +<tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2"> + <description>Generate SAM files from PSMs.</description> + <requirements> + <requirement type="package" version="3.3.1">r-base</requirement> + <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>--> + <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> + <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> + <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement> + <requirement type="package" version="1.11.1">r-devtools</requirement> + <requirement type="package" version="3.98_1.4">r-xml</requirement> + <requirement type="package" version="0.10.11">r-rmysql</requirement> + <requirement type="package" version="1.0.2">r-testthat</requirement> + <requirement type="package" version="0.1.0">r-getoptlong</requirement> + <requirement type="package" version="1.1.2">r-stringi</requirement> + <requirement type="package" version="1.1.0">r-stringr</requirement> + <requirement type="package" version="1.10.0">r-data.table</requirement> + <requirement type="package" version="0.4_10">r-sqldf</requirement> + <requirement type="package" version="0.6_6">r-gsubfn</requirement> + <requirement type="package" version="2.3_47">r-chron</requirement> + <requirement type="package" version="0.3.10">r-proto</requirement> + <requirement type="package" version="1.8.4">r-plyr</requirement> + <requirement type="package" version="1.1_0">r-fastmatch</requirement> + <requirement type="package" version="0.1.0">r-ahocorasicktrie</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + </stdio> + <command><![CDATA[ + Rscript --vanilla '$__tool_directory__/PSM2SAM.R' + + #if str($input.input_type) == "idpicker": + --idpDB="$input.input_file" + --searchEngineScore="$input.scoreColumn" + #else if str($input.input_type) == "peptideshaker": + --peptideShakerPsmReport="$input.input_file" + #else if str($input.input_type) == "pepxmltab": + --pepXmlTab="$input.input_file" + --searchEngineScore="$input.scoreColumn" + #end if + + --bam="$bam_file" + + #if str($variantAnnotation_file) != 'None': + --variantAnnotation="$variantAnnotation_file" + #end if + + #if str($genome_annotation.source) == "history": + --exon_anno="$genome_annotation.exonAnno" + --proteinseq="$genome_annotation.proteinSeq" + --procodingseq="$genome_annotation.proCodingSeq" + #else: + #set index_path = $genome_annotation.builtin.fields.path + --exon_anno="$index_path/exon_anno.RData" + --proteinseq="$index_path/proseq.RData" + --procodingseq="$index_path/procodingseq.RData" + #end if + 2>&1 +]]> + </command> + <inputs> + <conditional name="input"> + <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"> + <option value="idpicker">IDPicker idpDB</option> + <option value="peptideshaker">PeptideShaker PSM report</option> + <option value="pepxmltab">PepXmlTab</option> + </param> + <when value="idpicker"> + <param name="input_file" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs"> + <validator type="empty_field" message="This field is required."/> + </param> + <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. "MyriMatch:mvh")" size="60" label="Score Name"> + <validator type="empty_field" message="This field is required."/> + </param> + </when> + <when value="peptideshaker"> + <param name="input_file" type="data" format="tabular" help="A PeptideShaker PSM report to convert to SAM" label="Input PSMs"> + <validator type="empty_field" message="This field is required."/> + </param> + </when> + <when value="pepxmltab"> + <param name="input_file" type="data" format="tabular" help="A pepXmlTab file to convert to SAM" label="Input PSMs"> + <validator type="empty_field" message="This field is required."/> + </param> + <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. "mvh")" size="60" label="Score Name"> + <validator type="empty_field" message="This field is required."/> + </param> + </when> + </conditional> + <conditional name="genome_annotation"> + <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"> + <option value="builtin">Use a built-in genome annotation</option> + <option value="history">Use annotation from your history</option> + </param> + <when value="builtin"> + <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="customProDB"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No annotations are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> + <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" /> + <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> + </when> + </conditional> + <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"> + <validator type="empty_field" message="This field is required."/> + </param> + <param name="variantAnnotation_file" type="data" format="RData" help="A variant annotation .RData file from customProDB." label="Variant Annotation" optional="true" /> + </inputs> + <outputs> + <data format="sam" name="output_sam" from_work_dir="output.sam" label="${input.input_file.name.rsplit('.',1)[0]}.sam"/> + </outputs> + <tests> + <test> + <param name="input_type" value="idpicker" /> + <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" /> + <param name="scoreColumn" value="Myrimatch:MVH" /> + <param name="source" value="history" /> + <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" /> + <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" /> + <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" /> + <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" /> + <param name="variantAnnotation_file" value="hg19/hg19_variant_annotation.RData" dbkey="hg19" /> + <output name="output" file="idpicker_hg19_with_variants.sam" /> + </test> + <test> + <param name="input_type" value="idpicker" /> + <param name="input_file" value="hg19/test.idpDB" dbkey="hg19" /> + <param name="scoreColumn" value="Myrimatch:MVH" /> + <param name="source" value="history" /> + <param name="exonAnno" value="hg19/exon_anno.RData" dbkey="hg19" /> + <param name="proteinSeq" value="hg19/proseq.RData" dbkey="hg19" /> + <param name="proCodingSeq" value="hg19/procodingseq.RData" dbkey="hg19" /> + <param name="bam_file" value="hg19/hg19_headers.sam" dbkey="hg19" /> + <output name="output" file="idpicker_hg19_no_variants.sam" /> + </test> + <!--<test> + <param name="input_type" value="pepxmltab" /> + <param name="input_file" value="passedPSM.tab" dbkey="hg19" /> + <param name="scoreColumn" value="Myrimatch:MVH" /> + <param name="source" value="history" /> + <param name="exonAnno" value="gencode/exon_anno.RData" dbkey="hg19" /> + <param name="proteinSeq" value="gencode/proseq.RData" dbkey="hg19" /> + <param name="proCodingSeq" value="gencode/procodingseq.RData" dbkey="hg19" /> + <output name="output" file="pepXmlTab_gencode.sam" /> + </test>--> + <test> + <param name="input_type" value="peptideshaker" /> + <param name="input_file" value="mm10/test.psm-report" dbkey="mm9" /> + <param name="source" value="history" /> + <param name="exonAnno" value="mm10/exon_anno.RData" dbkey="mm9" /> + <param name="proteinSeq" value="mm10/proseq.RData" dbkey="mm9" /> + <param name="proCodingSeq" value="mm10/procodingseq.RData" dbkey="mm9" /> + <param name="bam_file" value="mm10/Sample_Mouse_pro-B_total.whole_exp.bam" dbkey="mm9" /> + <param name="variantAnnotation_file" value="mm10/mm10_variant_annotation.RData" dbkey="mm9" /> + <output name="output" file="peptideshaker_mm10.sam" /> + </test> + </tests> + <help> +**Description** + +Generate SAM files from confident peptide-spectrum-matches (PSMs). +</help> +</tool> \ No newline at end of file