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comparison baseline_generator.xml @ 5:048f8cdbb6d2 draft default tip

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author davidvanzessen
date Thu, 07 Aug 2014 10:19:53 -0400
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4:aa4b95abef11 5:048f8cdbb6d2
1 <tool id="baseline_fasta_generator" name="Baseline generator" version="1.0"> 1 <tool id="baseline_fasta_generator" name="Baseline generator" version="1.0">
2 <description>Generate baseline fasta file</description> 2 <description>Generate baseline fasta file</description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 wrapper.sh $in_file $reference $out_file 4 wrapper.sh "
5 #for $i, $input in enumerate($inputs)
6 ${input.in_file}
7 #end for
8 "
9 "
10 #for $i, $input in enumerate($inputs)
11 ${input.id}
12 #end for
13 "
14 $reference $out_file
5 </command> 15 </command>
6 <inputs> 16 <inputs>
7 <param name="in_file" type="data" label="Input excel or IMGT zip file" /> 17 <repeat name="inputs" title="inputs" min="1" default="1">
18 <param name="in_file" type="data" label="Input excel or IMGT zip file" />
19 <param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
20 </repeat>
8 <param name="reference" type="data" format="fasta" label="Reference fasta file" /> 21 <param name="reference" type="data" format="fasta" label="Reference fasta file" />
9 </inputs> 22 </inputs>
10 <outputs> 23 <outputs>
11 <data format="fasta" name="out_file" label = "Baseline generator on $in_file.name with $reference.name"/> 24 <data format="fasta" name="out_file" label = "Baseline generator on ${on_string} with $reference.name"/>
12 </outputs> 25 </outputs>
13 <help> 26 <help>
14 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. 27 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
15 28
16 Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504. 29 Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504.