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comparison shear_assemble.xml @ 4:a82400332451

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Use shear_wrapper.py to generate reference indexes when needed
author Jim Johnson <jj@umn.edu>
date Tue, 16 Jul 2013 12:38:48 -0500
parents ea76da1e7281
children aaaa5a071ff0
comparison
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3:630532975fa9 4:a82400332451
4 <requirement type="package" version="0.1.2">shear</requirement> 4 <requirement type="package" version="0.1.2">shear</requirement>
5 </requirements> 5 </requirements>
6 <!-- 6 <!--
7 <version_command></version_command> 7 <version_command></version_command>
8 --> 8 -->
9 <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar assemble -s $sdi_file 9 <command interpreter="python">
10 #if $genomeSource.refGenomeSource == 'indexed': 10 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command assemble
11 -f $genomeSource.ref_fastas.fields.path 11 -p $prefix
12 #else: 12 -s $sdi_file
13 -f $genomeSource.ref_fasta 13 #if $genomeSource.refGenomeSource == 'indexed':
14 #end if 14 -f $genomeSource.ref_fastas.fields.path
15 -o $output_fasta 15 #else:
16 -f $genomeSource.ref_fasta
17 #end if
18 -o $output_fasta
16 </command> 19 </command>
17 <inputs> 20 <inputs>
21 <param name="prefix" type="text" value="shear_assemble" label="Prefix for all generated files">
22 <validator type="regex" message="Prefix should start with a letter and contain only letter, digit, and '_' or '-' characters">[a-zA-Z0-9][_a-zA-Z0-9-]*</validator>
23 </param>
18 <param name="sdi_file" type="data" format="shear.sdi" label="SDI file produced by SHEAR's 'sv' command containing the SVs to use to create the new genomic sequence."/> 24 <param name="sdi_file" type="data" format="shear.sdi" label="SDI file produced by SHEAR's 'sv' command containing the SVs to use to create the new genomic sequence."/>
19 <!-- reference data --> 25 <!-- reference data -->
20 <conditional name="genomeSource"> 26 <conditional name="genomeSource">
21 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?"> 27 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
22 <option value="indexed">Use a cached reference genome</option> 28 <option value="indexed">Use a cached reference genome</option>
37 </inputs> 43 </inputs>
38 <stdio> 44 <stdio>
39 <exit_code range="1:" level="fatal" description="Error" /> 45 <exit_code range="1:" level="fatal" description="Error" />
40 </stdio> 46 </stdio>
41 <outputs> 47 <outputs>
42 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: personal genome" /> 48 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: ${prefix}.fa" />
43 </outputs> 49 </outputs>
44 <tests> 50 <tests>
45 <test> 51 <test>
46 <param name="sdi_file" ftype="shear.sdi" value="shear_sv.sdi"/> 52 <param name="prefix" value="shear_assembly" />
53 <param name="sdi_file" value="shear_sv.sdi" ftype="shear.sdi" />
47 <param name="refGenomeSource" value="history"/> 54 <param name="refGenomeSource" value="history"/>
48 <param name="ref_fasta" ftype="fasta" value="syn.fa"/> 55 <param name="ref_fasta" value="syn.fa" ftype="fasta" />
49 <output name="output_fasta" file="simulated-data.fa"/> 56 <output name="output_fasta" file="simulated-data.fa"/>
50 </test> 57 </test>
51 </tests> 58 </tests>
52 <help> 59 <help>
53 SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome. 60 SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome.