Mercurial > repos > davidvanzessen > report_clonality_igg
diff plotting_merged.xml @ 10:06777331fbd8 draft
Uploaded
author | davidvanzessen |
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date | Thu, 15 May 2014 09:27:22 -0400 |
parents | 08aa67564858 |
children | 866d22e60e60 |
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--- a/plotting_merged.xml Wed Mar 26 11:55:13 2014 -0400 +++ b/plotting_merged.xml Thu May 15 09:27:22 2014 -0400 @@ -1,17 +1,33 @@ <tool id="report_clonality_igg" name="Report Clonality" version="1.0"> <description> </description> <command interpreter="bash"> - r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" + r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection </command> <inputs> - <param name="in_file" format="tabular" type="data" label="Data to Process" /> - <param name="clonaltype_select" type="select" label="Clonal Type Definition"> - <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> - <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> - <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> - <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> - <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> - </param> + <param name="in_file" format="tabular" type="data" label="Data to Process" /> + <param name="clonaltype_select" type="select" label="Clonal Type Definition"> + <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> + <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> + <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> + <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> + <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> + </param> + + <param name="species" type="select" label="Species"> + <option value="human">Human</option> + <option value="mouse">Mouse</option> + </param> + + <param name="locus" type="select" label="Locus"> + <option value="igh">IGH</option> + <option value="igk">IGK</option> + <option value="igl">IGL</option> + </param> + + <param name="selection" type="select" label="Selection"> + <option value="unique">Unique (Based on clonaltype)</option> + <option value="all">All</option> + </param> </inputs> <outputs>