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comparison 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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5:862d0b2c3731 6:8540e2e45352
1 <<<<<<< HEAD
2 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
3 <description>mapper for full-length T- and B-cell repertoire sequencing
4 </description>
5 =======
6 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy1">
7 <description>mapper for full-length T- and B-cell repertoire sequencing</description>
8 <xrefs>
9 <xref type='bio.tools'>MiGMAP</xref>
10 </xrefs>
11 >>>>>>> d4217b609 (add bio.tools IDs until M)
12 <macros>
13 <token name="@TOOL_VERSION@">1.0.3</token>
14 </macros>
15 <requirements>
16 <requirement type="package" version="@TOOL_VERSION@">migmap</requirement>
17 </requirements>
18 <command detect_errors='aggressive'><![CDATA[
19 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
20 mkdir -p temp_db/igblast &&
21 ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
22 ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
23 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
24
25 #if $input.is_of_type('fasta') :
26 ln -s '$input' in.fa &&
27 #else if $input.is_of_type('fasta.gz') :
28 ln -s '$input' in.fa.gz &&
29 #else if $input.is_of_type('fastq') :
30 ln -s '$input' in.fq &&
31 #else if $input.is_of_type('fastq.gz') :
32 ln -s '$input' in.fq.gz
33 #end if
34
35 migmap
36 $allow_incomplete
37 $allow_no_cdr3
38 $allow_noncanonical
39 $allow_noncoding
40 $all_alleles
41 $by_read
42 #if str($qual_threshold):
43 -q $qual_threshold
44 #end if
45 -p "\${GALAXY_SLOTS:-4}"
46 --data-dir ./temp_db/igblast/
47 -S $species
48 -R $receptor_list
49 #if $input.is_of_type('fasta'):
50 in.fa
51 #else
52 in.fq
53 #end if
54 '$output'
55 ]]></command>
56 <inputs>
57 <param type="data" name="input" format="fasta,fastq"/>
58 <param type="select" name="species" label="Species" value='human'>
59 <option value='human' selected='true'>Human</option>
60 <option value='mouse'>Mouse</option>
61 <option value='rat'>Rat</option>
62 <option value='rabbit'>Rabbit</option>
63 <option value='rhesus_monkey'>Rhesus monkey</option>
64 </param>
65 <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
66 <option value='IGH' selected='true'>IGH</option>
67 <option value='IGL'>IGL</option>
68 <option value='IGK'>IGK</option>
69 <option value='TRA'>TRA</option>
70 <option value='TRB'>TRB</option>
71 <option value='TRG'>TRG</option>
72 <option value='TRD'>TRD</option>
73 </param>
74 <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
75 help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
76 <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
77 truevalue="--allow-incomplete" falsevalue=""/>
78 <param name="all_alleles" type="boolean"
79 label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
80 truevalue="--all-alleles" falsevalue=""/>
81 <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
82 truevalue="--allow-no-cdr3" falsevalue=""/>
83 <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
84 checked='false'
85 truevalue="--allow-noncanonical" falsevalue=""/>
86 <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
87 checked='false'
88 truevalue="--allow-noncoding" falsevalue=""/>
89 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
90 truevalue="--by-read" falsevalue=""/>
91 </inputs>
92 <outputs>
93 <data name="output" format="tabular"/>
94 </outputs>
95 <tests>
96 <test>
97 <param name="input" value="test_stop_codon.fa"/>
98 <param name="allow_noncoding" value="--allow-noncoding"/>
99 <param name="by_read" value="--by-read"/>
100 <param name="allow_noncanonical" value="--allow-noncanonical"/>
101 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
102 <param name="allow_incomplete" value="--allow-incomplete"/>
103 <param name="all_alleles" value="--all-alleles"/>
104 <output name="output" file="test_stop_codon.out"/>
105 </test>
106 <test>
107 <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
108 <param name="allow_noncoding" value="--allow-noncoding"/>
109 <param name="by_read" value="--by-read"/>
110 <param name="allow_noncanonical" value="--allow-noncanonical"/>
111 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
112 <param name="allow_incomplete" value="--allow-incomplete"/>
113 <param name="all_alleles" value="--all-alleles"/>
114 <output name="output" file="test_stop_codon.out" lines_diff="2"/>
115 </test>
116 <test>
117 <param name="allow_noncoding" value="--allow-noncoding"/>
118 <param name="by_read" value="--by-read"/>
119 <param name="input" value="test_out_of_frame.fa"/>
120 <output name="output" file="test_out_of_frame.out"/>
121 </test>
122 </tests>
123 <help><![CDATA[
124
125 This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
126 receptor libraries profiled using high-throughput sequencing
127
128 ]]></help>
129 <citations>
130 <citation type="bibtex">
131 @misc{githubmigmap,
132 author = {Shugay, Mikhail},
133 year = {2015},
134 title = {migmap},
135 publisher = {GitHub},
136 journal = {GitHub repository},
137 url = {https://github.com/mikessh/migmap},
138 }
139 </citation>
140 </citations>
141 </tool>