Mercurial > repos > iuc > migmap

annotate migmap.xml.orig @ 6:8540e2e45352 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:38:25 +0000
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6
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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1 <<<<<<< HEAD
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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2 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <description>mapper for full-length T- and B-cell repertoire sequencing
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 </description>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 =======
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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6 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy1">
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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7 <description>mapper for full-length T- and B-cell repertoire sequencing</description>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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8 <xrefs>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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9 <xref type='bio.tools'>MiGMAP</xref>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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10 </xrefs>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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11 >>>>>>> d4217b609 (add bio.tools IDs until M)
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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12 <macros>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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13 <token name="@TOOL_VERSION@">1.0.3</token>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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14 </macros>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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15 <requirements>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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16 <requirement type="package" version="@TOOL_VERSION@">migmap</requirement>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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17 </requirements>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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18 <command detect_errors='aggressive'><![CDATA[
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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19 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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20 mkdir -p temp_db/igblast &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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21 ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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22 ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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23 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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25 #if $input.is_of_type('fasta') :
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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26 ln -s '$input' in.fa &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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27 #else if $input.is_of_type('fasta.gz') :
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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28 ln -s '$input' in.fa.gz &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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29 #else if $input.is_of_type('fastq') :
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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30 ln -s '$input' in.fq &&
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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31 #else if $input.is_of_type('fastq.gz') :
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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32 ln -s '$input' in.fq.gz
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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33 #end if
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 migmap
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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36 $allow_incomplete
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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37 $allow_no_cdr3
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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38 $allow_noncanonical
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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39 $allow_noncoding
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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40 $all_alleles
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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41 $by_read
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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42 #if str($qual_threshold):
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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43 -q $qual_threshold
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44 #end if
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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45 -p "\${GALAXY_SLOTS:-4}"
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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46 --data-dir ./temp_db/igblast/
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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47 -S $species
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 -R $receptor_list
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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49 #if $input.is_of_type('fasta'):
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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50 in.fa
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 #else
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52 in.fq
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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53 #end if
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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54 '$output'
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 ]]></command>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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56 <inputs>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 <param type="data" name="input" format="fasta,fastq"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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58 <param type="select" name="species" label="Species" value='human'>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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59 <option value='human' selected='true'>Human</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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60 <option value='mouse'>Mouse</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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61 <option value='rat'>Rat</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62 <option value='rabbit'>Rabbit</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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63 <option value='rhesus_monkey'>Rhesus monkey</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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64 </param>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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66 <option value='IGH' selected='true'>IGH</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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67 <option value='IGL'>IGL</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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68 <option value='IGK'>IGK</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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69 <option value='TRA'>TRA</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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70 <option value='TRB'>TRB</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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71 <option value='TRG'>TRG</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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72 <option value='TRD'>TRD</option>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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73 </param>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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74 <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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75 help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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76 <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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77 truevalue="--allow-incomplete" falsevalue=""/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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78 <param name="all_alleles" type="boolean"
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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79 label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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80 truevalue="--all-alleles" falsevalue=""/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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81 <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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82 truevalue="--allow-no-cdr3" falsevalue=""/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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83 <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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84 checked='false'
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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85 truevalue="--allow-noncanonical" falsevalue=""/>
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86 <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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87 checked='false'
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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88 truevalue="--allow-noncoding" falsevalue=""/>
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89 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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90 truevalue="--by-read" falsevalue=""/>
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91 </inputs>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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92 <outputs>
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93 <data name="output" format="tabular"/>
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94 </outputs>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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95 <tests>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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96 <test>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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97 <param name="input" value="test_stop_codon.fa"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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98 <param name="allow_noncoding" value="--allow-noncoding"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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99 <param name="by_read" value="--by-read"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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100 <param name="allow_noncanonical" value="--allow-noncanonical"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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101 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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102 <param name="allow_incomplete" value="--allow-incomplete"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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103 <param name="all_alleles" value="--all-alleles"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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104 <output name="output" file="test_stop_codon.out"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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105 </test>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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106 <test>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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107 <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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108 <param name="allow_noncoding" value="--allow-noncoding"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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109 <param name="by_read" value="--by-read"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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110 <param name="allow_noncanonical" value="--allow-noncanonical"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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111 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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112 <param name="allow_incomplete" value="--allow-incomplete"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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113 <param name="all_alleles" value="--all-alleles"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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114 <output name="output" file="test_stop_codon.out" lines_diff="2"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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115 </test>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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116 <test>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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117 <param name="allow_noncoding" value="--allow-noncoding"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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118 <param name="by_read" value="--by-read"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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119 <param name="input" value="test_out_of_frame.fa"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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120 <output name="output" file="test_out_of_frame.out"/>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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121 </test>
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122 </tests>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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123 <help><![CDATA[
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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124
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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125 This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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126 receptor libraries profiled using high-throughput sequencing
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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127
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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128 ]]></help>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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129 <citations>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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130 <citation type="bibtex">
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131 @misc{githubmigmap,
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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132 author = {Shugay, Mikhail},
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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133 year = {2015},
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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134 title = {migmap},
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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135 publisher = {GitHub},
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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136 journal = {GitHub repository},
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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137 url = {https://github.com/mikessh/migmap},
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138 }
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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139 </citation>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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140 </citations>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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141 </tool>