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comparison customProDB.xml @ 12:2656b09d2046 draft

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author galaxyp
date Mon, 30 Jan 2017 09:43:57 -0500
parents 982fb2cde6c5
children 37cd89a40cea
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11:982fb2cde6c5 12:2656b09d2046
1 <tool id="custom_pro_db" name="CustomProDB" version="1.10.0"> 1 <tool id="custom_pro_db" name="CustomProDB" version="1.14.0">
2 <description>Generate protein FASTAs from exosome or transcriptome data</description> 2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
3 <requirements>
4 <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
5 </requirements>
3 <stdio> 6 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" /> 7 <exit_code range="1:" level="fatal" description="Job Failed" />
5 </stdio> 8 </stdio>
6 <command interpreter="Rscript --vanilla">customProDB.R 9 <command><![CDATA[
10 Rscript --vanilla '$__tool_directory__/customProDB.R'
11 --bam='$genome_annotation.bamInput'
12 --bai='${genome_annotation.bamInput.metadata.bam_index}'
13 --vcf='$genome_annotation.vcfInput'
14 --rpkmCutoff=$rpkmCutoff
15 --outputFile='${output_rpkm}'
7 16
8 --bam="$genome_annotation.bamInput" 17 #if str($genome_annotation.source) == 'history':
9 --bai="${genome_annotation.bamInput.metadata.bam_index}" 18 --exon_anno='$genome_annotation.exonAnno'
10 --vcf="$genome_annotation.vcfInput" 19 --proteinseq='$genome_annotation.proteinSeq'
11 --rpkmCutoff=$rpkmCutoff 20 --procodingseq='$genome_annotation.proCodingSeq'
12 --outputFile="${output_rpkm}" 21 --ids='$genome_annotation.ids'
13 22 #if str($genome_annotation.dbsnpInCoding) != 'None':
14 #if str($genome_annotation.source) == "history": 23 --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
15 --exon_anno="$genome_annotation.exonAnno"
16 --proteinseq="$genome_annotation.proteinSeq"
17 --procodingseq="$genome_annotation.proCodingSeq"
18 --ids="$genome_annotation.ids"
19 #if str($genome_annotation.dbsnpInCoding) != "None":
20 --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
21 #end if 24 #end if
22 #if str($genome_annotation.cosmic) != "None": 25 #if str($genome_annotation.cosmic) != 'None':
23 --cosmic="$genome_annotation.cosmic" 26 --cosmic='$genome_annotation.cosmic"
24 #end if 27 #end if
25 #else: 28 #else:
26 #set index_path = $genome_annotation.builtin.fields.path 29 #set index_path = $genome_annotation.builtin.fields.path
27 --exon_anno="$index_path/exon_anno.RData" 30 --exon_anno='$index_path/exon_anno.RData'
28 --proteinseq="$index_path/proseq.RData" 31 --proteinseq='$index_path/proseq.RData'
29 --procodingseq="$index_path/procodingseq.RData" 32 --procodingseq='$index_path/procodingseq.RData'
30 --ids="$index_path/ids.RData" 33 --ids='$index_path/ids.RData'
31 #if $genome_annotation.dbsnpInCoding: 34 #if $genome_annotation.dbsnpInCoding:
32 --dbsnpinCoding="$index_path/dbsnpinCoding.RData" 35 --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
33 #end if 36 #end if
34 #if $genome_annotation.cosmic: 37 #if $genome_annotation.cosmic:
35 --cosmic="$index_path/cosmic.RData" 38 --cosmic='$index_path/cosmic.RData'
36 #end if 39 #end if
37 #end if 40 #end if
38 41 2>1
39 2&gt;&amp;1</command> 42 ]]>
43 </command>
40 <inputs> 44 <inputs>
41 <conditional name="genome_annotation"> 45 <conditional name="genome_annotation">
42 <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"> 46 <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">
43 <option value="builtin">Use a built-in genome annotation</option> 47 <option value="builtin">Use a built-in genome annotation</option>
44 <option value="history">Use annotation from your history</option> 48 <option value="history">Use annotation from your history</option>
71 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> 75 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
72 <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" /> 76 <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
73 <param name="bamInput" type="data" format="bam" label="BAM file"> 77 <param name="bamInput" type="data" format="bam" label="BAM file">
74 <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" /> 78 <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" />
75 </param> 79 </param>
76 <param name="baiInput" type="data" format="bam_index" label="BAM Index file"> 80 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
77 <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" /> 81 <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" />
78 </param> 82 </param>-->
79 <param name="vcfInput" type="data" format="vcf" label="VCF file" /> 83 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
80 <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" /> 84 <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
81 <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" /> 85 <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
82 </when> 86 </when>
83 </conditional> 87 </conditional>
100 <output name="output_rpkm" file="test_rpkm.fasta" /> 104 <output name="output_rpkm" file="test_rpkm.fasta" />
101 <output name="output_snv" file="test_snv.fasta" /> 105 <output name="output_snv" file="test_snv.fasta" />
102 <output name="output_indel" file="test_indel.fasta" /> 106 <output name="output_indel" file="test_indel.fasta" />
103 </test> 107 </test>
104 </tests> 108 </tests>
105 <help> 109 <help><![CDATA[
106 **Description** 110 **Description**
107 111
108 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help> 112 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
113
114 ]]></help>
109 <citations> 115 <citations>
110 <citation type="doi">10.1093/bioinformatics/btt543</citation> 116 <citation type="doi">10.1093/bioinformatics/btt543</citation>
111 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub 117 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub
112 repository}, 118 repository},
113 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = 119 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =