Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 6:2ddb9a21f635 draft

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author davidvanzessen
date Tue, 01 Nov 2016 10:48:38 -0400
parents 012a738edf5a
children 4b695ca65213
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5:012a738edf5a 6:2ddb9a21f635
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 $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 $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>
64 <filter>naive_output_cond['naive_output'] == "yes"</filter> 64 <filter>naive_output_cond['naive_output'] == "yes"</filter>
65 </data> 65 </data>
66 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" > 66 <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> 67 <filter>naive_output_cond['naive_output'] == "yes"</filter>
68 </data> 68 </data>
69 <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>
71 </data>
69 </outputs> 72 </outputs>
70 <citations> 73 <citations>
71 <citation type="doi">10.1093/nar/gks457</citation> 74 <citation type="doi">10.1093/nar/gks457</citation>
72 <citation type="doi">10.1093/bioinformatics/btv359</citation> 75 <citation type="doi">10.1093/bioinformatics/btv359</citation>
73 </citations> 76 </citations>