Mercurial > repos > davidvanzessen > argalaxy_tools
comparison mutation_analysis.xml @ 57:16c7fc1c4bf8 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 18 Mar 2016 07:50:34 -0400 |
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| 56:2eb94c08e550 | 57:16c7fc1c4bf8 |
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| 1 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0"> | |
| 2 <description></description> | |
| 3 <command interpreter="bash"> | |
| 4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output $filter_uniques | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param name="in_file" type="data" label="IMGT zip file to be analysed" /> | |
| 8 <param name="method" type="select" label="Identification method" help="" > | |
| 9 <option value="custom" selected="true">custom</option> | |
| 10 <option value="blastn">blastn</option> | |
| 11 </param> | |
| 12 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" > | |
| 13 <option value="yes">yes</option> | |
| 14 <option value="no" selected="true">no</option> | |
| 15 </param> | |
| 16 <param name="functionality" type="select" label="Functionality filter" help="" > | |
| 17 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option> | |
| 18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option> | |
| 19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option> | |
| 20 <option value="dont_filter">Don't filter</option> | |
| 21 </param> | |
| 22 | |
| 23 <param name="unique" type="select" label="Remove duplicates based on" help="" > | |
| 24 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option> | |
| 25 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option> | |
| 26 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option> | |
| 27 <option value="AA.JUNCTION">AA.JUNCTION</option> | |
| 28 <option value="none">Don't remove duplicates</option> | |
| 29 </param> | |
| 30 <conditional name="naive_output_cond"> | |
| 31 <param name="naive_output" type="select" label="Output a file for naive analysis?"> | |
| 32 <option value="yes">Yes</option> | |
| 33 <option value="no" selected="true">No</option> | |
| 34 </param> | |
| 35 </conditional> | |
| 36 <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."> | |
| 37 <option value="yes">Yes</option> | |
| 38 <option value="no" selected="true">No</option> | |
| 39 <option value="keep">Keep uniques and filter out the duplicates</option> | |
| 40 </param> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 43 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> | |
| 44 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" > | |
| 45 <filter>naive_output_cond['naive_output'] == "yes"</filter> | |
| 46 </data> | |
| 47 </outputs> | |
| 48 <help> | |
| 49 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis. | |
| 50 </help> | |
| 51 <requirements> | |
| 52 <requirement type="package" version="1.0">blastn</requirement> | |
| 53 </requirements> | |
| 54 </tool> |