Mercurial > repos > galaxyp > custom_pro_db
diff customProDB.xml @ 6:61e45c111ef7 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author | galaxyp |
---|---|
date | Wed, 03 Feb 2016 12:37:47 -0500 |
parents | 6db27bef602f |
children | b83a4002aab1 |
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--- a/customProDB.xml Fri Jan 29 16:03:10 2016 -0500 +++ b/customProDB.xml Wed Feb 03 12:37:47 2016 -0500 @@ -5,34 +5,30 @@ </stdio> <command interpreter="Rscript --vanilla">customProDB.R - --bam="$bamInput" - --vcf="$vcfInput" - --outputFile="$output" + --bam="$genome_annotation.bamInput" + --bai="${genome_annotation.bamInput.metadata.bam_index}" + --vcf="$genome_annotation.vcfInput" + --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" #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" #end if 2>&1</command> <inputs> - <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM"> - <validator type="empty_field" message="This field is required."/> - </param> - <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls"> - <validator type="empty_field" message="This field is required."/> - </param> - <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 a genome from the history and build index</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"> @@ -41,29 +37,53 @@ <validator type="no_options" message="No annotations are available for the selected input dataset"/> </options> </param> + <param name="bamInput" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> + </param> + <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> + </param>--> + <param name="vcfInput" type="data" format="vcf" label="VCF file"> + <validator type="unspecified_build" /> + <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> + </param> </when> <when value="history"> - <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> - <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> - <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> + <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> + <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" /> + <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> + <param name="ids" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" /> + <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"> + <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 name="vcfInput" type="data" format="vcf" label="VCF file" /> </when> </conditional> </inputs> <outputs> - <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/> + <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/> + <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/> + <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/> </outputs> - <!--<tests> + <tests> <test> - <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" /> - <param name="scoreColumn" value="Myrimatch:MVH" /> - <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" /> + <param name="bamInput" value="test1_sort.bam" dbkey="hg19" /> + <param name="vcfInput" value="test1.vcf" dbkey="hg19" /> + <param name="source" value="history" /> + <param name="exonAnno" value="exon_anno.RData" /> + <param name="proteinSeq" value="proseq.RData" /> + <param name="proCodingSeq" value="procodingseq.RData" /> + <param name="ids" value="ids.RData" /> + <output name="output_rpkm" file="test_rpkm.fasta" /> + <output name="output_snv" file="test_snv.fasta" /> + <output name="output_indel" file="test_indel.fasta" /> </test> - <test> - <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" /> - <param name="scoreColumn" value="Myrimatch:MVH" /> - <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" /> - </test> - </tests>--> + </tests> <help> **Description**