Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 34:96c1276ceefe draft

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Uploaded
author davidvanzessen
date Fri, 16 Dec 2016 09:53:09 -0500
parents fe44a905aee9
children a24f8c93583a
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33:22fabe161cf3 34:96c1276ceefe
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_cond.naive_output $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 4 wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $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>