Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline
changeset 16:0b248a4f18a7 draft default tip
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 23 Jan 2014 04:23:42 -0500 |
| parents | c69d9262c66d |
| children | |
| files | combined.xml |
| diffstat | 1 files changed, 38 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/combined.xml Thu Jan 23 04:23:42 2014 -0500 @@ -0,0 +1,38 @@ +<tool id="igblastn_immunerepertoire_igg" name="igBLASTn ImmuneRepertoire" version="1.0"> + <description> </description> + <command interpreter="bash"> + combined.sh + #for $i, $f in enumerate($patients) + ${f.id} + #for $j, $g in enumerate($f.samples) + ${g.sample} + #end for + #end for + "$clonaltype_select" $out_file $out_file.files_path + </command> + <inputs> + <repeat name="patients" title="Patients" min="1" default="1"> + <repeat name="samples" title="Sample" min="1" default="1"> + <param name="sample" type="data" label="Sample to Process" /> + </repeat> + <param name="id" type="text" label="ID" /> + </repeat> + <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> + </inputs> + <outputs> + <data format="html" name="out_file" /> + </outputs> + <help> + The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them. + </help> + <requirements> + <requirement type="package" version="1.0.0">igBlastn</requirement> + </requirements> +</tool> +