Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality_igg.xml @ 47:d97e1421aa86 draft

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author davidvanzessen
date Wed, 27 Jan 2016 10:25:43 -0500
parents 4d201d22633d
children 5ba0377b7737
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46:fee06348bfad 47:d97e1421aa86
1 <tool id="report_clonality_igg" name="Report Clonality" version="1.0"> 1 <tool id="report_clonality_igg" name="Report Clonality" version="1.0">
2 <description> </description> 2 <description> </description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 #if $gene_selection.source == "imgtdb" 4 #if $gene_selection.source == "imgtdb"
5 report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method 5 report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method $filter_uniques
6 #else 6 #else
7 report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method 7 report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method $filter_uniques
8 #end if 8 #end if
9 </command> 9 </command>
10 <inputs> 10 <inputs>
11 <param name="in_file" format="tabular" type="data" label="Data to Process" /> 11 <param name="in_file" format="tabular" type="data" label="Data to Process" />
12 <param name="clonaltype" type="select" label="Clonal Type Definition (Needed for clonality calculation)"> 12 <param name="clonaltype" type="select" label="Clonal Type Definition (Needed for clonality calculation)">
13 <option value="none">Dont remove duplicates based on clonaltype</option> 13 <option value="none">Don't remove duplicates based on clonaltype</option>
14 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> 14 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
15 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> 15 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
16 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> 16 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
17 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> 17 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
18 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option> 18 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
93 <param name="clonality_method" type="select" label="Old clonality algorithm or the newer R package"> 93 <param name="clonality_method" type="select" label="Old clonality algorithm or the newer R package">
94 <option value="old">Old</option> 94 <option value="old">Old</option>
95 <option value="boyd">R Package</option> 95 <option value="boyd">R Package</option>
96 </param> 96 </param>
97 97
98 <param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
99 <option value="yes">Yes</option>
100 <option value="no">No</option>
101 </param>
102
98 </inputs> 103 </inputs>
99 <outputs> 104 <outputs>
100 <data format="html" name="out_file" /> 105 <data format="html" name="out_file" />
101 </outputs> 106 </outputs>
102 <requirements> 107 <requirements>