Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 20:ba2511ebd36a draft

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Uploaded
author davidvanzessen
date Mon, 28 Nov 2016 07:23:50 -0500
parents fff3c83ec9b8
children c0ecc31829bd
comparison
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19:fff3c83ec9b8 20:ba2511ebd36a
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_cond.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 $naive_output_all $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>
69 </data> 69 </data>
70 <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" > 70 <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" >
71 <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> 72 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
73 </data> 73 </data>
74 <data format="imgt_archive" name="naive_output_ca" label = "Naive input data from ${in_file.name}" > 74 <data format="imgt_archive" name="naive_output_all" label = "Naive input data from ${in_file.name}" >
75 <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> 76 <filter>class_filter_cond['class_filter'] == "101_101"</filter>
77 </data> 77 </data>
78 </outputs> 78 </outputs>
79 <citations> 79 <citations>