Mercurial > repos > iuc > migmap

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents 862d0b2c3731
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
1 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
2 <description>mapper for full-length T- and B-cell repertoire sequencing
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
3 </description>
6
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
4 <xrefs>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
5 <xref type="bio.tools">MiGMAP</xref>
8540e2e45352 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
6 </xrefs>
3
4570e5e2b4b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit ce007cd86035d1fdbcfa7105b593dcadc3e2cf30"
iuc
parents: 2
diff changeset
7 <macros>
4570e5e2b4b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit ce007cd86035d1fdbcfa7105b593dcadc3e2cf30"
iuc
parents: 2
diff changeset
8 <token name="@TOOL_VERSION@">1.0.3</token>
4570e5e2b4b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit ce007cd86035d1fdbcfa7105b593dcadc3e2cf30"
iuc
parents: 2
diff changeset
9 </macros>
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
10 <requirements>
3
4570e5e2b4b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit ce007cd86035d1fdbcfa7105b593dcadc3e2cf30"
iuc
parents: 2
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">migmap</requirement>
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
12 </requirements>
4
1c8b286f8c13 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit e32ce67ab5bbb46569f220489b72ecc11b7a0fd3"
iuc
parents: 3
diff changeset
13 <command detect_errors='aggressive'><![CDATA[
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
14 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
2
39a143860749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 60e2302cfac90d0c909ef61815aaaafaaad5816a
iuc
parents: 1
diff changeset
15 mkdir -p temp_db/igblast &&
39a143860749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 60e2302cfac90d0c909ef61815aaaafaaad5816a
iuc
parents: 1
diff changeset
16 ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
39a143860749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 60e2302cfac90d0c909ef61815aaaafaaad5816a
iuc
parents: 1
diff changeset
17 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
iuc
parents: 1
diff changeset
18 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
1
eb806186aa93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 9028fa28c7b3216926bf999dd21c5f156d1cc63e
iuc
parents: 0
diff changeset
19
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
20 #if $input.is_of_type('fasta') :
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
21 ln -s '$input' in.fa &&
5
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
22 #else if $input.is_of_type('fasta.gz') :
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
23 ln -s '$input' in.fa.gz &&
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
24 #else if $input.is_of_type('fastq') :
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
25 ln -s '$input' in.fq &&
5
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
26 #else if $input.is_of_type('fastq.gz') :
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
27 ln -s '$input' in.fq.gz
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
28 #end if
5
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
29
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
30 migmap
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
31 $allow_incomplete
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
32 $allow_no_cdr3
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
33 $allow_noncanonical
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
34 $allow_noncoding
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
35 $all_alleles
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
36 $by_read
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
37 #if str($qual_threshold):
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
38 -q $qual_threshold
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
39 #end if
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
40 -p "\${GALAXY_SLOTS:-4}"
1
eb806186aa93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 9028fa28c7b3216926bf999dd21c5f156d1cc63e
iuc
parents: 0
diff changeset
41 --data-dir ./temp_db/igblast/
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
42 -S $species
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
43 -R $receptor_list
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
44 #if $input.is_of_type('fasta'):
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
45 in.fa
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
46 #else
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
47 in.fq
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
48 #end if
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
49 '$output'
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
50 ]]></command>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
51 <inputs>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
52 <param type="data" name="input" format="fasta,fastq"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
53 <param type="select" name="species" label="Species" value='human'>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
54 <option value='human' selected='true'>Human</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
55 <option value='mouse'>Mouse</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
56 <option value='rat'>Rat</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
57 <option value='rabbit'>Rabbit</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
58 <option value='rhesus_monkey'>Rhesus monkey</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
59 </param>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
60 <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
61 <option value='IGH' selected='true'>IGH</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
62 <option value='IGL'>IGL</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
63 <option value='IGK'>IGK</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
64 <option value='TRA'>TRA</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
65 <option value='TRB'>TRB</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
66 <option value='TRG'>TRG</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
67 <option value='TRD'>TRD</option>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
68 </param>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
69 <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
70 help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
71 <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
72 truevalue="--allow-incomplete" falsevalue=""/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
73 <param name="all_alleles" type="boolean"
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
74 label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
75 truevalue="--all-alleles" falsevalue=""/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
76 <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
77 truevalue="--allow-no-cdr3" falsevalue=""/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
78 <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
79 checked='false'
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
80 truevalue="--allow-noncanonical" falsevalue=""/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
81 <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
82 checked='false'
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
83 truevalue="--allow-noncoding" falsevalue=""/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
84 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
85 truevalue="--by-read" falsevalue=""/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
86 </inputs>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
87 <outputs>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
88 <data name="output" format="tabular"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
89 </outputs>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
90 <tests>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
91 <test>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
92 <param name="input" value="test_stop_codon.fa"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
93 <param name="allow_noncoding" value="--allow-noncoding"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
94 <param name="by_read" value="--by-read"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
95 <param name="allow_noncanonical" value="--allow-noncanonical"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
96 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
97 <param name="allow_incomplete" value="--allow-incomplete"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
98 <param name="all_alleles" value="--all-alleles"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
99 <output name="output" file="test_stop_codon.out"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
100 </test>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
101 <test>
5
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
102 <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
103 <param name="allow_noncoding" value="--allow-noncoding"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
104 <param name="by_read" value="--by-read"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
105 <param name="allow_noncanonical" value="--allow-noncanonical"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
106 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
107 <param name="allow_incomplete" value="--allow-incomplete"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
108 <param name="all_alleles" value="--all-alleles"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
109 <output name="output" file="test_stop_codon.out" lines_diff="2"/>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
110 </test>
862d0b2c3731 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
iuc
parents: 4
diff changeset
111 <test>
0
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
112 <param name="allow_noncoding" value="--allow-noncoding"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
113 <param name="by_read" value="--by-read"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
114 <param name="input" value="test_out_of_frame.fa"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
115 <output name="output" file="test_out_of_frame.out"/>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
116 </test>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
117 </tests>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
118 <help><![CDATA[
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
119
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
120 This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
121 receptor libraries profiled using high-throughput sequencing
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
122
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
123 ]]></help>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
124 <citations>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
125 <citation type="bibtex">
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
126 @misc{githubmigmap,
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
127 author = {Shugay, Mikhail},
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
128 year = {2015},
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
129 title = {migmap},
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
130 publisher = {GitHub},
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
131 journal = {GitHub repository},
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
132 url = {https://github.com/mikessh/migmap},
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
133 }
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
134 </citation>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
135 </citations>
cbf4a6ffc369 planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa
iuc
parents:
diff changeset
136 </tool>