Mercurial > repos > galaxyp > custom_pro_db
diff customProDB.xml @ 11:982fb2cde6c5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
| author | galaxyp |
|---|---|
| date | Fri, 13 Jan 2017 12:18:32 -0500 |
| parents | ed65d110c1b5 |
| children | 2656b09d2046 |
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--- a/customProDB.xml Wed Jun 08 15:02:58 2016 -0400 +++ b/customProDB.xml Fri Jan 13 12:18:32 2017 -0500 @@ -1,110 +1,116 @@ -<tool id="custom_pro_db" name="CustomProDB" version="1.10.0"> - <description>Generate protein FASTAs from exosome or transcriptome data</description> - <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="$genome_annotation.vcfInput" - --rpkmCutoff=$rpkmCutoff - --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" - #end if - #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" - #if $genome_annotation.dbsnpInCoding: - --dbsnpinCoding="$index_path/dbsnpinCoding.RData" - #end if - #if $genome_annotation.cosmic: - --cosmic="$index_path/cosmic.RData" - #end if - #end if - -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"> - <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> - <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> - <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> - <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> - </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" /> - <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" /> - <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" /> - </when> - </conditional> - <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." /> - </inputs> - <outputs> - <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="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/> - </outputs> - <tests> - <test> - <param name="bamInput" value="test1_sort.bam" dbkey="hg19" /> - <param name="vcfInput" value="test1.vcf" dbkey="hg19" /> - <param name="source" value="history" /> - <param name="exonAnno" value="exon_anno.RData" /> - <param name="proteinSeq" value="proseq.RData" /> - <param name="proCodingSeq" value="procodingseq.RData" /> - <param name="ids" value="ids.RData" /> - <output name="output_rpkm" file="test_rpkm.fasta" /> - <output name="output_snv" file="test_snv.fasta" /> - <output name="output_indel" file="test_indel.fasta" /> - </test> - </tests> - <help> -**Description** - -Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). -</help> -</tool> \ No newline at end of file +<tool id="custom_pro_db" name="CustomProDB" version="1.10.0"> + <description>Generate protein FASTAs from exosome or transcriptome data</description> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + </stdio> + <command interpreter="Rscript --vanilla">customProDB.R + + --bam="$genome_annotation.bamInput" + --bai="${genome_annotation.bamInput.metadata.bam_index}" + --vcf="$genome_annotation.vcfInput" + --rpkmCutoff=$rpkmCutoff + --outputFile="${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="$genome_annotation.dbsnpInCoding" + #end if + #if str($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" + #if $genome_annotation.dbsnpInCoding: + --dbsnpinCoding="$index_path/dbsnpinCoding.RData" + #end if + #if $genome_annotation.cosmic: + --cosmic="$index_path/cosmic.RData" + #end if + #end if + +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"> + <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> + <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> + <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> + <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> + </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" /> + <param name="ids" type="data" format="RData" 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" /> + <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" /> + </when> + </conditional> + <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." /> + </inputs> + <outputs> + <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="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/> + </outputs> + <tests> + <test> + <param name="bamInput" value="test1_sort.bam" dbkey="hg19" /> + <param name="vcfInput" value="test1.vcf" dbkey="hg19" /> + <param name="source" value="history" /> + <param name="exonAnno" value="exon_anno.RData" /> + <param name="proteinSeq" value="proseq.RData" /> + <param name="proCodingSeq" value="procodingseq.RData" /> + <param name="ids" value="ids.RData" /> + <output name="output_rpkm" file="test_rpkm.fasta" /> + <output name="output_snv" file="test_snv.fasta" /> + <output name="output_indel" file="test_indel.fasta" /> + </test> + </tests> + <help> +**Description** + +Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt543</citation> + <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub +repository}, + year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = +{$sha1$}" --> + </citations> +</tool>