Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.xml @ 7:b83a4002aab1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Fri, 06 May 2016 15:56:07 -0400
parents 61e45c111ef7
children 328a1e3b5261
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6:61e45c111ef7 7:b83a4002aab1
6 <command interpreter="Rscript --vanilla">customProDB.R 6 <command interpreter="Rscript --vanilla">customProDB.R
7 7
8 --bam="$genome_annotation.bamInput" 8 --bam="$genome_annotation.bamInput"
9 --bai="${genome_annotation.bamInput.metadata.bam_index}" 9 --bai="${genome_annotation.bamInput.metadata.bam_index}"
10 --vcf="$genome_annotation.vcfInput" 10 --vcf="$genome_annotation.vcfInput"
11 --rpkmCutoff=$rpkmCutoff
11 --outputFile="${output_rpkm}" 12 --outputFile="${output_rpkm}"
12 13
13 #if str($genome_annotation.source) == "history": 14 #if str($genome_annotation.source) == "history":
14 --exon_anno="$genome_annotation.exonAnno" 15 --exon_anno="$genome_annotation.exonAnno"
15 --proteinseq="$genome_annotation.proteinSeq" 16 --proteinseq="$genome_annotation.proteinSeq"
62 <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> 63 <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
63 </param> 64 </param>
64 <param name="vcfInput" type="data" format="vcf" label="VCF file" /> 65 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
65 </when> 66 </when>
66 </conditional> 67 </conditional>
68 <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
67 </inputs> 69 </inputs>
68 <outputs> 70 <outputs>
69 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/> 71 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
70 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/> 72 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
71 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/> 73 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>