Mercurial > repos > galaxyp > custom_pro_db
changeset 12:2656b09d2046 draft
Uploaded
author | galaxyp |
---|---|
date | Mon, 30 Jan 2017 09:43:57 -0500 |
parents | 982fb2cde6c5 |
children | 37cd89a40cea |
files | ._customProDB.xml customProDB.xml |
diffstat | 2 files changed, 34 insertions(+), 28 deletions(-) [+] |
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--- a/customProDB.xml Fri Jan 13 12:18:32 2017 -0500 +++ b/customProDB.xml Mon Jan 30 09:43:57 2017 -0500 @@ -1,42 +1,46 @@ -<tool id="custom_pro_db" name="CustomProDB" version="1.10.0"> +<tool id="custom_pro_db" name="CustomProDB" version="1.14.0"> <description>Generate protein FASTAs from exosome or transcriptome data</description> + <requirements> + <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement> + </requirements> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> </stdio> - <command interpreter="Rscript --vanilla">customProDB.R - - --bam="$genome_annotation.bamInput" - --bai="${genome_annotation.bamInput.metadata.bam_index}" - --vcf="$genome_annotation.vcfInput" + <command><![CDATA[ + Rscript --vanilla '$__tool_directory__/customProDB.R' + --bam='$genome_annotation.bamInput' + --bai='${genome_annotation.bamInput.metadata.bam_index}' + --vcf='$genome_annotation.vcfInput' --rpkmCutoff=$rpkmCutoff - --outputFile="${output_rpkm}" + --outputFile='${output_rpkm}' - #if str($genome_annotation.source) == "history": - --exon_anno="$genome_annotation.exonAnno" - --proteinseq="$genome_annotation.proteinSeq" - --procodingseq="$genome_annotation.proCodingSeq" - --ids="$genome_annotation.ids" - #if str($genome_annotation.dbsnpInCoding) != "None": - --dbsnpinCoding="$genome_annotation.dbsnpInCoding" + #if str($genome_annotation.source) == 'history': + --exon_anno='$genome_annotation.exonAnno' + --proteinseq='$genome_annotation.proteinSeq' + --procodingseq='$genome_annotation.proCodingSeq' + --ids='$genome_annotation.ids' + #if str($genome_annotation.dbsnpInCoding) != 'None': + --dbsnpinCoding='$genome_annotation.dbsnpInCoding' #end if - #if str($genome_annotation.cosmic) != "None": - --cosmic="$genome_annotation.cosmic" + #if str($genome_annotation.cosmic) != 'None': + --cosmic='$genome_annotation.cosmic" #end if #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" - --ids="$index_path/ids.RData" + --exon_anno='$index_path/exon_anno.RData' + --proteinseq='$index_path/proseq.RData' + --procodingseq='$index_path/procodingseq.RData' + --ids='$index_path/ids.RData' #if $genome_annotation.dbsnpInCoding: - --dbsnpinCoding="$index_path/dbsnpinCoding.RData" + --dbsnpinCoding='$index_path/dbsnpinCoding.RData' #end if #if $genome_annotation.cosmic: - --cosmic="$index_path/cosmic.RData" + --cosmic='$index_path/cosmic.RData' #end if #end if - -2>&1</command> + 2>1 +]]> + </command> <inputs> <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"> @@ -73,9 +77,9 @@ <param name="bamInput" type="data" format="bam" label="BAM file"> <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> </param> - <param name="baiInput" type="data" format="bam_index" label="BAM Index file"> + <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file"> <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> - </param> + </param>--> <param name="vcfInput" type="data" format="vcf" label="VCF file" /> <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" /> <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" /> @@ -102,10 +106,12 @@ <output name="output_indel" file="test_indel.fasta" /> </test> </tests> - <help> + <help><![CDATA[ **Description** -Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help> +Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). + + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btt543</citation> <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub