Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 18:949a30f04d9b draft

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Uploaded
author davidvanzessen
date Mon, 28 Nov 2016 04:41:22 -0500
parents 61d0a6318711
children fff3c83ec9b8
comparison
equal deleted inserted replaced
17:b95fa7e426c3 18:949a30f04d9b
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_class">CDR3 (nt), C region</option> 32 <option value="CDR3.IMGT.seq,best_match_class">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" selected="true">Don't remove duplicates</option> 34 <option value="Sequence.ID" selected="true">Don't remove duplicates</option>
35 </param> 35 </param>
36 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" > 36 <conditional name="class_filter_cond">
37 <option value="70_70" selected="true">>70% class and >70% subclass</option> 37 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
38 <option value="60_55">>60% class and >55% subclass</option> 38 <option value="70_70" selected="true">>70% class and >70% subclass</option>
39 <option value="70_0">>70% class</option> 39 <option value="60_55">>60% class and >55% subclass</option>
40 <option value="60_0">>60% class</option> 40 <option value="70_0">>70% class</option>
41 <option value="101_101">Do not assign (sub)class</option> 41 <option value="60_0">>60% class</option>
42 </param> 42 <option value="101_101">Do not assign (sub)class</option>
43 </param>
44 </conditional>
43 <conditional name="naive_output_cond"> 45 <conditional name="naive_output_cond">
44 <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?">
45 <option value="yes">Yes</option> 47 <option value="yes">Yes</option>
46 <option value="no" selected="true">No</option> 48 <option value="no" selected="true">No</option>
47 </param> 49 </param>
57 </inputs> 59 </inputs>
58 <outputs> 60 <outputs>
59 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/> 61 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
60 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" > 62 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
61 <filter>naive_output_cond['naive_output'] == "yes"</filter> 63 <filter>naive_output_cond['naive_output'] == "yes"</filter>
64 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
62 </data> 65 </data>
63 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" > 66 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
64 <filter>naive_output_cond['naive_output'] == "yes"</filter> 67 <filter>naive_output_cond['naive_output'] == "yes"</filter>
68 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
65 </data> 69 </data>
66 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" > 70 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
67 <filter>naive_output_cond['naive_output'] == "yes"</filter> 71 <filter>naive_output_cond['naive_output'] == "yes"</filter>
72 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
68 </data> 73 </data>
69 <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" > 74 <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" >
70 <filter>naive_output_cond['naive_output'] == "yes"</filter> 75 <filter>naive_output_cond['naive_output'] == "yes"</filter>
76 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
77 </data>
78 <data format="imgt_archive" name="naive_output_ca" label = "Naive input data from ${in_file.name}" >
79 <filter>naive_output_cond['naive_output'] == "yes"</filter>
80 <filter>class_filter_cond['class_filter'] == "101_101"</filter>
71 </data> 81 </data>
72 </outputs> 82 </outputs>
73 <citations> 83 <citations>
74 <citation type="doi">10.1093/nar/gks457</citation> 84 <citation type="doi">10.1093/nar/gks457</citation>
75 <citation type="doi">10.1093/bioinformatics/btv359</citation> 85 <citation type="doi">10.1093/bioinformatics/btv359</citation>