Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 49:f5fe63533c58 draft

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author davidvanzessen
date Thu, 11 May 2017 10:21:39 -0400
parents 64711f461c8e
children 75ee66a691a0
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48:c5295dd10dfc 49:f5fe63533c58
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 #if str ( $filter_unique.filter_unique_select ) == "remove":
5 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_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast
6 #else:
7 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_unique.filter_unique_select 2 $class_filter_cond.class_filter $empty_region_filter $fast
8 #end if
5 </command> 9 </command>
6 <inputs> 10 <inputs>
7 <param name="in_file" type="data" label="IMGT zip file to be analysed" /> 11 <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="" > 12 <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> 13 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
14 <param name="functionality" type="select" label="Functionality filter" help="" > 18 <param name="functionality" type="select" label="Functionality filter" help="" >
15 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option> 19 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
16 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option> 20 <option value="unproductive">Unproductive (Unproductive and Unproductive 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="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
18 </param> 22 </param>
19 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example."> 23 <conditional name="filter_unique">
20 <option value="remove" selected="true">Remove uniques (Based on nucleotide sequence + C)</option> 24 <param name="filter_unique_select" type="select" label="Filter unique sequences" help="See below for an example.">
21 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option> 25 <option value="remove" selected="true">Remove uniques (Based on nucleotide sequence + C)</option>
22 <option value="no">No</option> 26 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
23 </param> 27 <option value="no">No</option>
28 </param>
29 <when value="remove">
30 <param name="filter_unique_clone_count" size="4" type="integer" label="How many sequences should be in a group to keep 1 of them" value="2" min="2"/>
31 </when>
32 </conditional>
24 <param name="unique" type="select" label="Remove duplicates based on" help="" > 33 <param name="unique" type="select" label="Remove duplicates based on" help="" >
25 <option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option> 34 <option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option>
26 <option value="VGene,CDR3.IMGT.AA">Top.V.Gene, CDR3 (AA)</option> 35 <option value="VGene,CDR3.IMGT.AA">Top.V.Gene, CDR3 (AA)</option>
27 <option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option> 36 <option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option>
28 <option value="CDR3.IMGT.AA">CDR3 (AA)</option> 37 <option value="CDR3.IMGT.AA">CDR3 (AA)</option>