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annotate migmap.xml @ 2:39a143860749 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 60e2302cfac90d0c909ef61815aaaafaaad5816a
author iuc
date Mon, 17 Jun 2019 07:52:51 -0400
parents eb806186aa93
children 4570e5e2b4b4
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1 <tool id="migmap" name="MiGMAP" version="1.0.2.2">
0
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2 <description>mapper for full-length T- and B-cell repertoire sequencing
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="1.0.2">migmap</requirement>
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6 </requirements>
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7 <command detect_errors='exit_code'><![CDATA[
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8 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
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9 mkdir -p temp_db/igblast &&
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10 ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
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11 ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
39a143860749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 60e2302cfac90d0c909ef61815aaaafaaad5816a
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12 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
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13
0
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14 #if $input.is_of_type('fasta') :
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15 ln -s '$input' in.fa &&
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16 #else
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17 ln -s '$input' in.fq &&
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18 #end if
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19 migmap
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20 $allow_incomplete
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21 $allow_no_cdr3
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22 $allow_noncanonical
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23 $allow_noncoding
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24 $all_alleles
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25 $by_read
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26 #if str($qual_threshold):
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27 -q $qual_threshold
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28 #end if
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29 -p "\${GALAXY_SLOTS:-4}"
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30 --data-dir ./temp_db/igblast/
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31 -S $species
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32 -R $receptor_list
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33 #if $input.is_of_type('fasta'):
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34 in.fa
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35 #else
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36 in.fq
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37 #end if
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38 '$output'
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39 ]]></command>
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40 <inputs>
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41 <param type="data" name="input" format="fasta,fastq"/>
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42 <param type="select" name="species" label="Species" value='human'>
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43 <option value='human' selected='true'>Human</option>
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44 <option value='mouse'>Mouse</option>
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45 <option value='rat'>Rat</option>
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46 <option value='rabbit'>Rabbit</option>
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47 <option value='rhesus_monkey'>Rhesus monkey</option>
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48 </param>
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49 <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
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50 <option value='IGH' selected='true'>IGH</option>
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51 <option value='IGL'>IGL</option>
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52 <option value='IGK'>IGK</option>
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53 <option value='TRA'>TRA</option>
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54 <option value='TRB'>TRB</option>
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55 <option value='TRG'>TRG</option>
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56 <option value='TRD'>TRD</option>
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57 </param>
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58 <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
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59 help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
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60 <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
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61 truevalue="--allow-incomplete" falsevalue=""/>
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62 <param name="all_alleles" type="boolean"
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63 label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
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64 truevalue="--all-alleles" falsevalue=""/>
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65 <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
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66 truevalue="--allow-no-cdr3" falsevalue=""/>
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67 <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
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68 checked='false'
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69 truevalue="--allow-noncanonical" falsevalue=""/>
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70 <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
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71 checked='false'
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72 truevalue="--allow-noncoding" falsevalue=""/>
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73 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
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74 truevalue="--by-read" falsevalue=""/>
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75 </inputs>
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76 <outputs>
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77 <data name="output" format="tabular"/>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="input" value="test_stop_codon.fa"/>
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82 <param name="allow_noncoding" value="--allow-noncoding"/>
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83 <param name="by_read" value="--by-read"/>
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84 <param name="allow_noncanonical" value="--allow-noncanonical"/>
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85 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
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86 <param name="allow_incomplete" value="--allow-incomplete"/>
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87 <param name="all_alleles" value="--all-alleles"/>
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88 <output name="output" file="test_stop_codon.out"/>
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89 </test>
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90 <test>
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91 <param name="allow_noncoding" value="--allow-noncoding"/>
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92 <param name="by_read" value="--by-read"/>
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93 <param name="input" value="test_out_of_frame.fa"/>
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94 <output name="output" file="test_out_of_frame.out"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98
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99 This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
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100 receptor libraries profiled using high-throughput sequencing
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101
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102 ]]></help>
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103 <citations>
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104 <citation type="bibtex">
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105 @misc{githubmigmap,
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106 author = {Shugay, Mikhail},
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107 year = {2015},
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108 title = {migmap},
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109 publisher = {GitHub},
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110 journal = {GitHub repository},
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111 url = {https://github.com/mikessh/migmap},
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112 }
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113 </citation>
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114 </citations>
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115 </tool>