Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 5:012a738edf5a draft

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author davidvanzessen
date Tue, 01 Nov 2016 10:15:37 -0400
parents faae21ba5c63
children 2ddb9a21f635
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4:477e95b098fd 5:012a738edf5a
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 $filter_uniques $class_filter $empty_region_filter 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 $filter_uniques $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>
31 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option> 31 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
32 <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option> 32 <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option>
33 <option value="CDR3.IMGT.seq">CDR3 (nt)</option> 33 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
34 <option value="Sequence.ID">Don't remove duplicates</option> 34 <option value="Sequence.ID">Don't remove duplicates</option>
35 </param> 35 </param>
36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" > 36 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
37 <option value="70_70" selected="true">>70% class and >70% subclass</option> 37 <option value="70_70" selected="true">>70% class and >70% subclass</option>
38 <option value="60_55">>60% class and >55% subclass</option> 38 <option value="60_55">>60% class and >55% subclass</option>
39 <option value="70_0">>70% class</option> 39 <option value="70_0">>70% class</option>
40 <option value="60_0">>60% class</option> 40 <option value="60_0">>60% class</option>
41 <option value="101_101">Do not assign (sub)class</option> 41 <option value="101_101">Do not assign (sub)class</option>
44 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> 44 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
45 <option value="yes">Yes</option> 45 <option value="yes">Yes</option>
46 <option value="no" selected="true">No</option> 46 <option value="no" selected="true">No</option>
47 </param> 47 </param>
48 </conditional> 48 </conditional>
49
50
51 <param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" >
52 <option value="yes">Yes</option>
53 <option value="no" selected="true">No</option>
54 </param>
55
56
49 </inputs> 57 </inputs>
50 <outputs> 58 <outputs>
51 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/> 59 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
52 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" > 60 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
53 <filter>naive_output_cond['naive_output'] == "yes"</filter> 61 <filter>naive_output_cond['naive_output'] == "yes"</filter>