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1 <tool id="report_clonality_igg" name="Report Clonality" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
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5 </command>
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6 <inputs>
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7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
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8 <param name="clonaltype" type="select" label="Clonal Type Definition">
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9 <option value="none">Dont remove duplicates based on clonaltype</option>
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10 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
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11 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
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12 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
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13 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
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14 <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>
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15 </param>
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16
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17 <param name="species" type="select" label="Species">
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18 <option value="human">Human</option>
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19 <option value="mouse">Mouse</option>
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20 </param>
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21
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22 <param name="locus" type="select" label="Locus">
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23 <option value="igh">IGH</option>
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24 <option value="igk">IGK</option>
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25 <option value="igl">IGL</option>
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26 <option value="trb">TRB</option>
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27 <option value="tra">TRA</option>
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28 <option value="trg">TRG</option>
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29 <option value="trd">TRD</option>
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30 </param>
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31
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32 <param name="filterproductive" type="select" label="Filter out the unproductive sequences">
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33 <option value="yes">Yes</option>
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34 <option value="no">No</option>
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35 </param>
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36
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37 </inputs>
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38 <outputs>
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39 <data format="html" name="out_file" />
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40 </outputs>
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41 <help>
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42 **INPUT**
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43
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44 One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool
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45
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46 **OUTPUT**
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47
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48 It generates the following result:
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49 </help>
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50 </tool>
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