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annotate migmap.xml @ 5:862d0b2c3731 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
author iuc
date Mon, 29 Mar 2021 22:16:12 +0000
parents 1c8b286f8c13
children 8540e2e45352
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862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
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1 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
0
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2 <description>mapper for full-length T- and B-cell repertoire sequencing
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3 </description>
3
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4 <macros>
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5 <token name="@TOOL_VERSION@">1.0.3</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">migmap</requirement>
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9 </requirements>
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10 <command detect_errors='aggressive'><![CDATA[
0
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11 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
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12 mkdir -p temp_db/igblast &&
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13 ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
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14 ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
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15 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
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16
0
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17 #if $input.is_of_type('fasta') :
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18 ln -s '$input' in.fa &&
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19 #else if $input.is_of_type('fasta.gz') :
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
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20 ln -s '$input' in.fa.gz &&
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
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21 #else if $input.is_of_type('fastq') :
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22 ln -s '$input' in.fq &&
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23 #else if $input.is_of_type('fastq.gz') :
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
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24 ln -s '$input' in.fq.gz
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25 #end if
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26
0
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27 migmap
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28 $allow_incomplete
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29 $allow_no_cdr3
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30 $allow_noncanonical
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31 $allow_noncoding
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32 $all_alleles
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33 $by_read
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34 #if str($qual_threshold):
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35 -q $qual_threshold
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36 #end if
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37 -p "\${GALAXY_SLOTS:-4}"
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38 --data-dir ./temp_db/igblast/
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39 -S $species
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40 -R $receptor_list
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41 #if $input.is_of_type('fasta'):
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42 in.fa
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43 #else
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44 in.fq
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45 #end if
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46 '$output'
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47 ]]></command>
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48 <inputs>
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49 <param type="data" name="input" format="fasta,fastq"/>
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50 <param type="select" name="species" label="Species" value='human'>
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51 <option value='human' selected='true'>Human</option>
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52 <option value='mouse'>Mouse</option>
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53 <option value='rat'>Rat</option>
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54 <option value='rabbit'>Rabbit</option>
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55 <option value='rhesus_monkey'>Rhesus monkey</option>
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56 </param>
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57 <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
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58 <option value='IGH' selected='true'>IGH</option>
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59 <option value='IGL'>IGL</option>
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60 <option value='IGK'>IGK</option>
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61 <option value='TRA'>TRA</option>
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62 <option value='TRB'>TRB</option>
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63 <option value='TRG'>TRG</option>
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64 <option value='TRD'>TRD</option>
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65 </param>
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66 <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
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67 help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
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68 <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
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69 truevalue="--allow-incomplete" falsevalue=""/>
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70 <param name="all_alleles" type="boolean"
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71 label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
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72 truevalue="--all-alleles" falsevalue=""/>
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73 <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
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74 truevalue="--allow-no-cdr3" falsevalue=""/>
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75 <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
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76 checked='false'
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77 truevalue="--allow-noncanonical" falsevalue=""/>
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78 <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
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79 checked='false'
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80 truevalue="--allow-noncoding" falsevalue=""/>
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81 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
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82 truevalue="--by-read" falsevalue=""/>
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83 </inputs>
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84 <outputs>
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85 <data name="output" format="tabular"/>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="input" value="test_stop_codon.fa"/>
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90 <param name="allow_noncoding" value="--allow-noncoding"/>
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91 <param name="by_read" value="--by-read"/>
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92 <param name="allow_noncanonical" value="--allow-noncanonical"/>
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93 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
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94 <param name="allow_incomplete" value="--allow-incomplete"/>
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95 <param name="all_alleles" value="--all-alleles"/>
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96 <output name="output" file="test_stop_codon.out"/>
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97 </test>
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98 <test>
5
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99 <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
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100 <param name="allow_noncoding" value="--allow-noncoding"/>
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101 <param name="by_read" value="--by-read"/>
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102 <param name="allow_noncanonical" value="--allow-noncanonical"/>
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103 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
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104 <param name="allow_incomplete" value="--allow-incomplete"/>
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105 <param name="all_alleles" value="--all-alleles"/>
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106 <output name="output" file="test_stop_codon.out" lines_diff="2"/>
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107 </test>
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108 <test>
0
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109 <param name="allow_noncoding" value="--allow-noncoding"/>
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110 <param name="by_read" value="--by-read"/>
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111 <param name="input" value="test_out_of_frame.fa"/>
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112 <output name="output" file="test_out_of_frame.out"/>
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113 </test>
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114 </tests>
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115 <help><![CDATA[
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116
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117 This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
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118 receptor libraries profiled using high-throughput sequencing
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119
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120 ]]></help>
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121 <citations>
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122 <citation type="bibtex">
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123 @misc{githubmigmap,
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124 author = {Shugay, Mikhail},
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125 year = {2015},
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126 title = {migmap},
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127 publisher = {GitHub},
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128 journal = {GitHub repository},
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129 url = {https://github.com/mikessh/migmap},
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130 }
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131 </citation>
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132 </citations>
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133 </tool>