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comparison migmap.xml @ 0:b2f1cf977ca9 draft

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planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
author iuc
date Sat, 30 Sep 2017 09:33:24 -0400
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children fbbe507e692b
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-1:000000000000 0:b2f1cf977ca9
1 <tool id="migmap" name="MiGMAP" version="1.0.2.1">
2 <description>mapper for full-length T- and B-cell repertoire sequencing
3 </description>
4 <requirements>
5 <requirement type="package" version="1.0.2">migmap</requirement>
6 </requirements>
7 <command detect_errors='exit_code'><![CDATA[
8 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
9 #if $input.is_of_type('fasta') :
10 ln -s '$input' in.fa &&
11 #else
12 ln -s '$input' in.fq &&
13 #end if
14 migmap
15 $allow_incomplete
16 $allow_no_cdr3
17 $allow_noncanonical
18 $allow_noncoding
19 $all_alleles
20 $by_read
21 #if str($qual_threshold):
22 -q $qual_threshold
23 #end if
24 -p "\${GALAXY_SLOTS:-4}"
25 --data-dir "\${IGBLAST_PATH}/../share/igblast"
26 -S $species
27 -R $receptor_list
28 --report '$report'
29 #if $input.is_of_type('fasta'):
30 in.fa
31 #else
32 in.fq
33 #end if
34 '$output'
35 ]]></command>
36 <inputs>
37 <param type="data" name="input" format="fasta,fastq"/>
38 <param type="select" name="species" label="Species" value='human'>
39 <option value='human' selected='true'>Human</option>
40 <option value='mouse'>Mouse</option>
41 <option value='rat'>Rat</option>
42 <option value='rabbit'>Rabbit</option>
43 <option value='rhesus_monkey'>Rhesus monkey</option>
44 </param>
45 <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
46 <option value='IGH' selected='true'>IGH</option>
47 <option value='IGL'>IGL</option>
48 <option value='IGK'>IGK</option>
49 <option value='TRA'>TRA</option>
50 <option value='TRB'>TRB</option>
51 <option value='TRG'>TRG</option>
52 <option value='TRD'>TRD</option>
53 </param>
54 <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
55 help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
56 <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
57 truevalue="--allow-incomplete" falsevalue=""/>
58 <param name="all_alleles" type="boolean"
59 label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
60 truevalue="--all-alleles" falsevalue=""/>
61 <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
62 truevalue="--allow-no-cdr3" falsevalue=""/>
63 <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
64 checked='false'
65 truevalue="--allow-noncanonical" falsevalue=""/>
66 <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
67 checked='false'
68 truevalue="--allow-noncoding" falsevalue=""/>
69 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
70 truevalue="--by-read" falsevalue=""/>
71 </inputs>
72 <outputs>
73 <data name="output" format="tabular"/>
74 <data name="report" format="txt"/>
75 </outputs>
76 <tests>
77 <test>
78 <param name="input" value="test_stop_codon.fa"/>
79 <param name="allow_noncoding" value="--allow-noncoding"/>
80 <param name="by_read" value="--by-read"/>
81 <param name="allow_noncanonical" value="--allow-noncanonical"/>
82 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
83 <param name="allow_incomplete" value="--allow-incomplete"/>
84 <param name="all_alleles" value="--all-alleles"/>
85 <output name="output" file="test_stop_codon.out"/>
86 </test>
87 <test>
88 <param name="allow_noncoding" value="--allow-noncoding"/>
89 <param name="by_read" value="--by-read"/>
90 <param name="input" value="test_out_of_frame.fa"/>
91 <output name="output" file="test_out_of_frame.out"/>
92 </test>
93 </tests>
94 <help><![CDATA[
95
96 This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
97 receptor libraries profiled using high-throughput sequencing
98
99 ]]></help>
100 <citations>
101 <citation type="bibtex">
102 @misc{githubmigmap,
103 author = {Shugay, Mikhail},
104 year = {2015},
105 title = {migmap},
106 publisher = {GitHub},
107 journal = {GitHub repository},
108 url = {https://github.com/mikessh/migmap},
109 }
110 </citation>
111 </citations>
112 </tool>