Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 19:fff3c83ec9b8 draft

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author davidvanzessen
date Mon, 28 Nov 2016 05:15:16 -0500
parents 949a30f04d9b
children ba2511ebd36a
comparison
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18:949a30f04d9b 19:fff3c83ec9b8
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
2 <description></description> 2 <description></description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $filter_uniques $class_filter $empty_region_filter $fast 4 wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
5 </command> 5 </command>
6 <inputs> 6 <inputs>
7 <param name="in_file" type="data" label="IMGT zip file to be analysed" /> 7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
8 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" > 8 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
9 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option> 9 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
46 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> 46 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
47 <option value="yes">Yes</option> 47 <option value="yes">Yes</option>
48 <option value="no" selected="true">No</option> 48 <option value="no" selected="true">No</option>
49 </param> 49 </param>
50 </conditional> 50 </conditional>
51
52
53 <param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" > 51 <param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" >
54 <option value="yes">Yes</option> 52 <option value="yes">Yes</option>
55 <option value="no" selected="true">No</option> 53 <option value="no" selected="true">No</option>
56 </param> 54 </param>
57
58
59 </inputs> 55 </inputs>
60 <outputs> 56 <outputs>
61 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/> 57 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
62 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" > 58 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
63 <filter>naive_output_cond['naive_output'] == "yes"</filter> 59 <filter>naive_output_cond['naive_output'] == "yes"</filter>