Mercurial > repos > iuc > mixcr_analyze

annotate mixcr_analyze.xml @ 0:d38cfb922f95 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
author iuc
date Thu, 10 Oct 2019 18:03:22 -0400
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d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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1 <tool id="mixcr_analyze" name="MiXCR Analyze" version="@VERSION@.0">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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2 <description>immuno clonotyes from sequence data</description>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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3 <macros>
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4 <import>mixcr_macros.xml</import>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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5 </macros>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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6 <expand macro="requirements" />
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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7 <command detect_errors="exit_code"><![CDATA[
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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8 #import os.path
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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9 #import re
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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10 #def clean(name)
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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11 #set $base_name = $os.path.basename($name)
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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12 #set $name_clean = re.sub('[^\w\-_\.]', '_', $base_name)
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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13 #return $name_clean
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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14 #end def
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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15 #if $imgt.library_selector == 'history':
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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16 #set $libname = $re.sub('.gz$','',$clean($imgt.library.name))
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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17 ln -s -f '$imgt.library' $libname &&
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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18 #end if
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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19 #if str( $fastq_input.fastq_input_selector ) == "paired":
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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20 #set $fq1 = $clean($fastq_input.fastq_input1.name)
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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21 ln -s -f '$fastq_input.fastq_input1' $fq1 &&
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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22 #set $fq2 = $clean($fastq_input.fastq_input2.name)
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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23 ln -s -f '$fastq_input.fastq_input2' $fq2 &&
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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24 #else:
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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25 #set $fq1 = $clean($fastq_input.fastq_input1.name)
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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26 ln -s -f '$fastq_input.fastq_input1' $fq1 &&
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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27 #end if
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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28 mixcr analyze $analyze.pipeline --starting-material $starting_material
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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29 #if $analyze.pipeline == 'amplicon':
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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30 --5-end $analyze.primers5end
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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31 --3-end $analyze.primers3end
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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32 --adapters $analyze.adapters
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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33 #end if
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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34 #if $imgt.library_selector == 'history':
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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35 --align "--library $libname"
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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36 #set $taxonId = str($imgt.species).split(':')[0]
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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37 --species $taxonId
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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38 ## #elif $imgt.library_selector == 'cached':
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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39 #else
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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40 --species $imgt.species
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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41 #end if
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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42 $contig_assembly $impute_germline_on_export $only_productive
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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43 --receptor-type $receptor_type
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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44 #if str( $fastq_input.fastq_input_selector ) == "paired":
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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45 $fq1 $fq2
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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46 #else:
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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47 $fq1
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48 #end if
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49 mixcr_analysis
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50 ]]></command>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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51 <inputs>
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52 <conditional name="analyze">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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53 <param name="pipeline" type="select" label="amplicon or shotgun data" help="">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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54 <option value="amplicon">amplicon: enriched targeted TCR/IG libraries (5’RACE, Amplicon, Multiplex, etc)</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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55 <option value="shotgun">shotgun: non-enriched RNA-seq or non-targeted genomic data</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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56 </param>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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57 <when value="amplicon">
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58 <param name="primers5end" type="select" label="5’-end of the library.">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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59 <help>
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60 There are two possible values:
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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61 no-v-primers — no V gene primers (e.g. 5’RACE with template switch oligo or a like),
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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62 v-primers — V gene single primer / multiple.
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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63 </help>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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64 <option value="no-v-primers">no-v-primers</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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65 <option value="v-primers">v-primers</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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66 </param>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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67 <param name="primers3end" type="select" label="3’-end of the library.">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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68 <help>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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69 There are three possible values:
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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70 j-primers — J gene single primer / multiplex,
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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71 j-c-intron-primers — J-C intron single primer / multiplex,
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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72 c-primers — C gene single primer / multiplex (e.g. IGHC primers specific to different immunoglobulin isotypes).
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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73 </help>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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74 <option value="j-primers">j-primers</option>
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75 <option value="j-c-intron-primers">j-c-intron-primers</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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76 <option value="c-primers">c-primers</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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77 </param>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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78 <param name="adapters" type="select" label="Presence of PCR primers and/or adapter sequences">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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79 <help>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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80 If sequences of primers used for PCR or adapters are present in sequencing data,
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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81 it may influence the accuracy of V, J and C gene segments identification and CDR3 mapping.
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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82 </help>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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83 <option value="adapters-present">adapters-present</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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84 <option value="no-adapters">no-adapters</option>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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85 </param>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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86 </when>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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87 <when value="shotgun"/>
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88 </conditional>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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89 <param name="starting_material" type="select" label="Type of starting material: RNA or DNA" help="">
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iuc
parents:
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90 <option value="rna">RNA</option>
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iuc
parents:
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91 <option value="dna">DNA</option>
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iuc
parents:
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92 </param>
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iuc
parents:
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93 <conditional name="fastq_input">
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iuc
parents:
diff changeset
94 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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iuc
parents:
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95 <option value="single">single-end fastq</option>
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iuc
parents:
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96 <option value="paired">paired-end fastq</option>
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iuc
parents:
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97 </param>
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iuc
parents:
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98 <when value="paired">
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iuc
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99 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Select first set of reads" help="Specify dataset with forward reads"/>
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iuc
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100 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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iuc
parents:
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101 </when>
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iuc
parents:
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102 <when value="single">
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iuc
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103 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" label="Select sequence dataset" help="Specify dataset with single reads"/>
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iuc
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104 </when>
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iuc
parents:
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105 </conditional>
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iuc
parents:
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106 <conditional name="imgt">
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iuc
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107 <param name="library_selector" type="select" label="Library selector" help="Select between paired and single end data">
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iuc
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108 <option value="builtin">MiXCR builtin library</option>
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109 <!-- <option value="cached">repseqio IMGT library</option> -->
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iuc
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110 <option value="history">history repseqio IMGT library</option>
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iuc
parents:
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111 </param>
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iuc
parents:
diff changeset
112 <when value="builtin">
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iuc
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113 <param name="species" type="text" label="Species">
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114 <option value="9606">HomoSapiens</option>
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iuc
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115 <option value="MusMusculus">MusMusculus</option>
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iuc
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116 <option value="rat">rat</option>
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parents:
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117 </param>
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118 </when>
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iuc
parents:
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119 <!--
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120 <when value="cached">
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iuc
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121 <param name="library" type="select" label="repseqio IMGT library">
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iuc
parents:
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122 <options from_data_table="imgt_library">
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iuc
parents:
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123 <column name="name" index="1"/>
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iuc
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124 <column name="value" index="2"/>
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125 </options>
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126 </param>
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iuc
parents:
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127 <param name="species" type="select" label="Species">
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iuc
parents:
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128 <options from_data_table="imgt_library">
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iuc
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129 <column name="name" index="3"/>
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iuc
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130 <column name="value" index="3"/>
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iuc
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131 <filter type="param_value" ref="library" column="2" />
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iuc
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132 <filter type="multiple_splitter" column="3" separator=","/>
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133 </options>
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134 </param>
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135 </when>
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iuc
parents:
diff changeset
136 -->
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iuc
parents:
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137 <when value="history">
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iuc
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138 <param name="library" type="data" format="imgt.json" label="repseqio IMGT library">
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
iuc
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139 <help><![CDATA[
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iuc
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140 Data coming from IMGT server may be used for academic research only,
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iuc
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141 provided that it is referred to IMGT®, and cited as:MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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142
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143 MiXCR is free for academic and non-profit use (see License).
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144 "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."
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145 ]]></help>
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146 </param>
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iuc
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147 <param name="species" type="select" label="Species">
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148 <options>
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149 <filter type="data_meta" ref="library" key="taxon_names" />
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150 </options>
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151 </param>
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iuc
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152 </when>
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iuc
parents:
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153 </conditional>
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154 <param name="contig_assembly" type="boolean" truevalue="--contig-assembly" falsevalue="" checked="false" label="Assemble full receptor sequences." help="This option may slow down the computation."/>
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parents:
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155 <param name="impute_germline_on_export" type="boolean" truevalue="--impute-germline-on-export" falsevalue="" checked="false" label="Use germline segments (printed with lowercase letters) for uncovered gene features"/>
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156 <param name="only_productive" type="boolean" truevalue="--only-productive" falsevalue="" checked="false" label="Filter out-of-frame and stop-codons in export"/>
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iuc
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157 <param name="receptor_type" type="select" label="Dedicated receptor type for analysis">
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iuc
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158 <option value="xcr" selected="true">xcr (all T- and B-cell receptor chains are analyzed)</option>
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iuc
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159 <option value="tcr">tcr</option>
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iuc
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160 <option value="bcr">bcr</option>
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iuc
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161 <option value="tra">tra</option>
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162 <option value="trb">trb</option>
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163 <option value="trg">trg</option>
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164 <option value="trd">trd</option>
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165 <option value="igh">igh</option>
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166 <option value="igk">igk</option>
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167 <option value="igl">igl</option>
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168 </param>
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169 </inputs>
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170 <outputs>
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171 <data name="report" format="txt" label="${tool.name} on ${on_string}: report" from_work_dir="mixcr_analysis.report"/>
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172 <data name="clonotypes" format="tabular" label="${tool.name} on ${on_string}: clonotypes.ALL" from_work_dir="mixcr_analysis.clonotypes.ALL.txt">
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173 <actions>
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174 <action name="comment_lines" type="metadata" default="1" />
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iuc
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175 <action name="column_names" type="metadata" default="cloneId,cloneCount,cloneFraction,targetSequences,targetQualities,allVHitsWithScore,allDHitsWithScore,allJHitsWithScore,allCHitsWithScore,allVAlignments,allDAlignments,allJAlignments,allCAlignments,nSeqFR1,minQualFR1,nSeqCDR1,minQualCDR1,nSeqFR2,minQualFR2,nSeqCDR2,minQualCDR2,nSeqFR3,minQualFR3,nSeqCDR3,minQualCDR3,nSeqFR4,minQualFR4,aaSeqFR1,aaSeqCDR1,aaSeqFR2,aaSeqCDR2,aaSeqFR3,aaSeqCDR3,aaSeqFR4,refPoints" />
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176 </actions>
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177 </data>
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178 </outputs>
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179 <tests>
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180 <test>
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181 <conditional name="analyze">
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182 <param name="pipeline" value="shotgun"/>
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183 </conditional>
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184 <param name="starting_material" value="rna"/>
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185 <conditional name="fastq_input">
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186 <param name="fastq_input_selector" value="paired"/>
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187 <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/>
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188 <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/>
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189 </conditional>
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190 <conditional name="imgt">
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191 <param name="library_selector" value="builtin"/>
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192 <param name="species" value="9606"/>
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193 </conditional>
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194 <param name="contig_assembly" value="True"/>
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195 <param name="impute_germline_on_export" value="True"/>
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196 <param name="only_productive" value="False"/>
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197 <param name="receptor_type" value="xcr"/>
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198 <output name="report">
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199 <assert_contents>
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200 <has_text text="Final clonotype count" />
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201 </assert_contents>
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202 </output>
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203 <output name="clonotypes">
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204 <assert_contents>
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205 <has_text text="CARDDGGGKGDYGRLW" />
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206 </assert_contents>
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207 </output>
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208 </test>
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209 <test>
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210 <conditional name="analyze">
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211 <param name="pipeline" value="amplicon"/>
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212 <param name="primers5end" value="v-primers"/>
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213 <param name="primers3end" value="j-primers"/>
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214 <param name="adapters" value="no-adapters"/>
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215 </conditional>
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216 <param name="starting_material" value="rna"/>
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217 <conditional name="fastq_input">
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218 <param name="fastq_input_selector" value="paired"/>
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219 <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/>
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220 <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/>
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221 </conditional>
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222 <conditional name="imgt">
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223 <param name="library_selector" value="builtin"/>
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224 <param name="species" value="9606"/>
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225 </conditional>
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226 <param name="contig_assembly" value="True"/>
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227 <param name="impute_germline_on_export" value="True"/>
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228 <param name="only_productive" value="False"/>
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229 <param name="receptor_type" value="xcr"/>
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230 <output name="report">
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231 <assert_contents>
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232 <has_text text="Final clonotype count" />
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233 </assert_contents>
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234 </output>
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235 <output name="clonotypes">
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236 <assert_contents>
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237 <has_text text="CARDDGGGKGDYGRLW" />
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238 </assert_contents>
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239 </output>
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240 </test>
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241
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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242 </tests>
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243 <help><![CDATA[
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244 **MiXCR** **a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data**
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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245
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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246 MiXCR_ is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR_ efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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247
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248 **MiXCR is free for academic and non-profit use** (see License_).
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249
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250 This tool runs the MiXCR_ analyze_ pipeline.
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251 Generally, there two distinct types of library preparation which correspond to the two analyze pipelines:
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252
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253 - analyze_ amplicon_ for analysis of targeted TCR/IG library amplification (5’RACE, Amplicon, Multiplex, etc).
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254 - analyze_ shotgun_ for analysis of random fragments (RNA-Seq, Exome-Seq, etc).
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255
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256
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257 MiXCR_ has builtin libraries for human, mouse and rat. Additional compiled IMGT_ libraries can be imported into your Galaxy history as datatype: *imgt.json* from: https://github.com/repseqio/library-imgt/releases
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258
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259 NOTE: The imgt.201822-5.sv4.json.gz release has the rattus genus taxonId:10114 for rat, whereas the mixcr builtin library has the rattus norvegicus species taxId:10116 for rat. If you encounter imgt library loading errors from mixcr, you may have to substitute 10116 for 10114 in the imgt.201822-5.sv4.json.gz file.
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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260
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261 **Data coming from IMGT server may be used for academic research only**, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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262
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263 .. _MiXCR: https://mixcr.readthedocs.io/en/latest/index.html
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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264 .. _analyze: https://mixcr.readthedocs.io/en/latest/analyze.html
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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265 .. _amplicon: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-targeted-tcr-ig-libraries
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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266 .. _shotgun: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-non-enriched-or-random-fragments
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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267 .. _License: https://mixcr.readthedocs.io/en/latest/license.html#license
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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268 .. _IMGT: https://github.com/repseqio/library-imgt/releases
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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269 ]]></help>
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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270 <expand macro="citations" />
d38cfb922f95 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2"
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271 </tool>