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1 <tool id="shm_csr" name="SHM & CSR pipeline" version="1.0">
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2 <description></description>
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3 <command interpreter="bash">
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6
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4 wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $filter_uniques $class_filter $empty_region_filter $fast
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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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8 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
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9 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
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10 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
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11 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
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12 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
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13 </param>
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14 <param name="functionality" type="select" label="Functionality filter" help="" >
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15 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
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16 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
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17 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
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18 </param>
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19 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
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20 <option value="remove" selected="true">Remove uniques (Based on nucleotide sequence + C)</option>
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21 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
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22 <option value="no">No</option>
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23 </param>
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24 <param name="unique" type="select" label="Remove duplicates based on" help="" >
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25 <option value="VGene,AA.JUNCTION,best_match">Top.V.Gene, CDR3 (AA), C region</option>
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26 <option value="VGene,AA.JUNCTION">Top.V.Gene, CDR3 (AA)</option>
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27 <option value="AA.JUNCTION,best_match">CDR3 (AA), C region</option>
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28 <option value="AA.JUNCTION">CDR3 (AA)</option>
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29
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30 <option value="VGene,CDR3.IMGT.seq,best_match" selected="true">Top.V.Gene, CDR3.nt.Seq, C region</option>
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31 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
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32 <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option>
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33 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
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34 <option value="Sequence.ID" selected="true">Don't remove duplicates</option>
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35 </param>
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36 <param name="class_filter" type="select" label="Human 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">>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 <option value="101_101">Do not assign (sub)class</option>
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42 </param>
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43 <conditional name="naive_output_cond">
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44 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
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45 <option value="yes">Yes</option>
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46 <option value="no" selected="true">No</option>
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47 </param>
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48 </conditional>
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49
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50
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51 <param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" >
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52 <option value="yes">Yes</option>
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53 <option value="no" selected="true">No</option>
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54 </param>
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55
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56
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57 </inputs>
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58 <outputs>
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59 <data format="html" name="out_file" label = "SHM & CSR on ${in_file.name}"/>
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60 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
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61 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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62 </data>
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63 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
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64 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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65 </data>
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66 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
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67 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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68 </data>
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69 <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" >
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70 <filter>naive_output_cond['naive_output'] == "yes"</filter>
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71 </data>
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72 </outputs>
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73 <citations>
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74 <citation type="doi">10.1093/nar/gks457</citation>
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75 <citation type="doi">10.1093/bioinformatics/btv359</citation>
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76 </citations>
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77 <help>
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78 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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79
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80 +--------------------------+
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81 | unique filter |
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82 +--------+--------+--------+
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83 | values | remove | keep |
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84 +--------+--------+--------+
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85 | A | A | A |
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86 +--------+--------+--------+
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87 | A | B | B |
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88 +--------+--------+--------+
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89 | B | D | C |
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90 +--------+--------+--------+
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91 | B | | D |
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92 +--------+--------+--------+
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93 | C | | |
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94 +--------+--------+--------+
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95 | D | | |
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96 +--------+--------+--------+
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97 | D | | |
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98 +--------+--------+--------+
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99
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100 </help>
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101 </tool>
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