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comparison customProDB.xml @ 3:7e078d4e40f8 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, 29 Jan 2016 14:26:25 -0500
parents e6f488178a45
children 6db27bef602f
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2:e6f488178a45 3:7e078d4e40f8
2 <description>Generate protein FASTAs from exosome or transcriptome data</description> 2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
3 <stdio> 3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" /> 4 <exit_code range="1:" level="fatal" description="Job Failed" />
5 </stdio> 5 </stdio>
6 <command interpreter="Rscript --vanilla">PSM2SAM.R 6 <command interpreter="Rscript --vanilla">PSM2SAM.R
7 #if str($input).strip() != "": 7
8 --passedPSM="$input" 8 --bam="$bamInput"
9 #end if 9 --vcf="$vcfInput"
10 #if str($scoreColumn).strip() != "": 10 --outputFile="$output"
11 --XScolumn="$scoreColumn" 11
12 #end if 12 #if str($genome_annotation.source) == "history":
13 #if str($optionalUserInput.exonAnno).strip() != "None": 13 --exon_anno="$genome_annotation.exonAnno"
14 --exon_anno="$optionalUserInput.exonAnno" 14 --proteinseq="$genome_annotation.proteinSeq"
15 #end if 15 --procodingseq="$genome_annotation.proCodingSeq"
16 #if str($optionalUserInput.proteinSeq).strip() != "None": 16 #else:
17 --proteinseq="$optionalUserInput.proteinSeq" 17 #set index_path = $genome_annotation.builtin.fields.path
18 #end if 18 --exon_anno="$index_path/exon_anno.RData"
19 #if str($optionalUserInput.proCodingSeq).strip() != "None": 19 --proteinseq="$index_path/proseq.RData"
20 --procodingseq="$optionalUserInput.proCodingSeq" 20 --procodingseq="$index_path/procodingseq.RData"
21 #end if
22 #if str($optionalUserInput.header).strip() != "None":
23 --header="$optionalUserInput.header"
24 #end if
25 #if str($output).strip() != "":
26 --OutputFile="$output"
27 #end if 21 #end if
28 22
29 2&gt;&amp;1</command> 23 2&gt;&amp;1</command>
30 <inputs> 24 <inputs>
31 <param name="input" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAMs"> 25 <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
32 <validator type="empty_field" message="This field is required."/> 26 <validator type="empty_field" message="This field is required."/>
33 </param> 27 </param>
34 <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls"> 28 <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
35 <validator type="empty_field" message="This field is required."/> 29 <validator type="empty_field" message="This field is required."/>
36 </param> 30 </param>
37 <conditional name="optionalUserInput"> 31
38 <param name="optionalUserInputCondition" type="boolean" label="Override Default Exon Annotation and Coding Sequences" /> 32 <conditional name="genome_annotation">
39 <when value="true"> 33 <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">
40 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> 34 <option value="builtin">Use a built-in genome annotation</option>
41 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> 35 <option value="history">Use a genome from the history and build index</option>
42 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> 36 </param>
37 <when value="builtin">
38 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
39 <options from_data_table="customProDB">
40 <filter type="sort_by" column="2"/>
41 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
42 </options>
43 </param>
43 </when> 44 </when>
44 <when value="false"> 45 <when value="history">
46 <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" />
47 <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" />
48 <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" />
45 </when> 49 </when>
46 </conditional> 50 </conditional>
47 </inputs> 51 </inputs>
48 <outputs> 52 <outputs>
49 <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/> 53 <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>