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1 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
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2 <description></description>
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3 <command interpreter="bash">
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4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter
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5 </command>
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6 <inputs>
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7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
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19
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8 <param name="method" type="select" label="Identification method" help="" >
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9 <option value="custom" selected="true">custom</option>
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10 <option value="blastn">blastn</option>
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11 </param>
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12 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
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13 <option value="yes">yes</option>
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14 <option value="no" selected="true">no</option>
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15 </param>
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16 <param name="functionality" type="select" label="Functionality filter" help="" >
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17 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option>
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18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
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19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
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20 <option value="dont_filter">Don't filter</option>
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21 </param>
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22 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
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23 <option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
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24 <option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
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25 <option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
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26 <option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
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27 <option value="no" selected="true">No</option>
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28 </param>
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29 <param name="unique" type="select" label="Remove duplicates based on" help="" >
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30 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
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31 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
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32 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
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33 <option value="AA.JUNCTION">AA.JUNCTION</option>
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34 <option value="none">Don't remove duplicates</option>
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35 </param>
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36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" >
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37 <option value="70_70" selected="true">>70% class and >70% subclass</option>
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38 <option value="60_55" selected="true">>60% class and >55% subclass</option>
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39 <option value="70_0">>70% class</option>
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40 <option value="60_0">>60% class</option>
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41 </param>
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42 <conditional name="naive_output_cond">
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43 <param name="naive_output" type="select" label="Output a file for naive analysis?">
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44 <option value="yes">Yes</option>
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45 <option value="no" selected="true">No</option>
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46 </param>
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47 </conditional>
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
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51 <data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
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52 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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53 </data>
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54 <data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
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55 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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56 </data>
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57 <data format="tabular" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
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58 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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59 </data>
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60 </outputs>
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61 <help>
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62 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
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63
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64 +--------------------------+
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65 | unique filter |
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66 +--------+--------+--------+
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67 | values | remove | keep |
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68 +--------+--------+--------+
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69 | A | A | A |
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70 +--------+--------+--------+
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71 | A | B | B |
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72 +--------+--------+--------+
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73 | B | D | C |
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74 +--------+--------+--------+
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75 | B | | D |
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76 +--------+--------+--------+
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77 | C | | |
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78 +--------+--------+--------+
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79 | D | | |
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80 +--------+--------+--------+
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81 | D | | |
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82 +--------+--------+--------+
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83
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84 </help>
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46
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85 <requirements>
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86 <requirement type="package" version="1.0">blastn</requirement>
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87 </requirements>
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88 </tool>
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