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comparison shm_csr.xml @ 1:faae21ba5c63 draft

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author davidvanzessen
date Tue, 25 Oct 2016 07:28:43 -0400
parents c33d93683a09
children 012a738edf5a
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0:c33d93683a09 1:faae21ba5c63
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} ${include_fr1} $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
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="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option> 10 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
10 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option> 11 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
11 <option value="FR2">FR2: include CDR2,FR3 in filters</option> 12 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
12 </param> 13 </param>
13 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
14 <option value="yes">yes</option>
15 <option value="no" selected="true">no</option>
16 </param>
17 <param name="functionality" type="select" label="Functionality filter" help="" > 14 <param name="functionality" type="select" label="Functionality filter" help="" >
18 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option> 15 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
19 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option> 16 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
20 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option> 17 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
21 <option value="dont_filter">Don't filter</option>
22 </param> 18 </param>
23 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example."> 19 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
24 <option value="remove">Remove uniques (Based on nucleotide sequence + C)</option> 20 <option value="remove">Remove uniques (Based on nucleotide sequence + C)</option>
25 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option> 21 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
26 <option value="no" selected="true">No</option> 22 <option value="no" selected="true">No</option>
40 <param name="class_filter" type="select" label="Class/Subclass filter" help="" > 36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" >
41 <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>
42 <option value="60_55">>60% class and >55% subclass</option> 38 <option value="60_55">>60% class and >55% subclass</option>
43 <option value="70_0">>70% class</option> 39 <option value="70_0">>70% class</option>
44 <option value="60_0">>60% class</option> 40 <option value="60_0">>60% class</option>
45 <option value="101_101">No class</option> 41 <option value="101_101">Do not assign (sub)class</option>
46 </param> 42 </param>
47 <conditional name="naive_output_cond"> 43 <conditional name="naive_output_cond">
48 <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?">
49 <option value="yes">Yes</option> 45 <option value="yes">Yes</option>
50 <option value="no" selected="true">No</option> 46 <option value="no" selected="true">No</option>