Mercurial > repos > davidvanzessen > report_clonality_igg
changeset 18:6a8ec7c022dd draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 16 Dec 2014 03:33:36 -0500 |
| parents | ff84987df4f8 |
| children | c5256a227d2d |
| files | RScript.r plotting_merged.xml r_wrapper.sh report_clonality_igg.xml |
| diffstat | 2 files changed, 50 insertions(+), 50 deletions(-) [+] |
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--- a/plotting_merged.xml Tue Dec 16 03:28:57 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -<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" $species $locus $filterproductive - </command> - <inputs> - <param name="in_file" format="tabular" type="data" label="Data to Process" /> - <param name="clonaltype" type="select" label="Clonal Type Definition"> - <option value="none">Dont remove duplicates based on clonaltype</option> - <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> - <option value="trb">TRB</option> - <option value="tra">TRA</option> - <option value="trg">TRG</option> - <option value="trd">TRD</option> - </param> - - <param name="filterproductive" type="select" label="Filter out the unproductive sequences"> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - - </inputs> - <outputs> - <data format="html" name="out_file" /> - </outputs> - <help> -**INPUT** - -One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool - -**OUTPUT** - -It generates the following result: - </help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality_igg.xml Tue Dec 16 03:33:36 2014 -0500 @@ -0,0 +1,50 @@ +<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" $species $locus $filterproductive + </command> + <inputs> + <param name="in_file" format="tabular" type="data" label="Data to Process" /> + <param name="clonaltype" type="select" label="Clonal Type Definition"> + <option value="none">Dont remove duplicates based on clonaltype</option> + <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> + <option value="trb">TRB</option> + <option value="tra">TRA</option> + <option value="trg">TRG</option> + <option value="trd">TRD</option> + </param> + + <param name="filterproductive" type="select" label="Filter out the unproductive sequences"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + + </inputs> + <outputs> + <data format="html" name="out_file" /> + </outputs> + <help> +**INPUT** + +One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool + +**OUTPUT** + +It generates the following result: + </help> +</tool>