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comparison migmap.xml @ 1:fbbe507e692b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 9028fa28c7b3216926bf999dd21c5f156d1cc63e
author iuc
date Sat, 04 Aug 2018 12:22:14 -0400
parents b2f1cf977ca9
children 6ad9d48a512e
comparison
equal deleted inserted replaced
0:b2f1cf977ca9 1:fbbe507e692b
1 <tool id="migmap" name="MiGMAP" version="1.0.2.1"> 1 <tool id="migmap" name="MiGMAP" version="1.0.2.2">
2 <description>mapper for full-length T- and B-cell repertoire sequencing 2 <description>mapper for full-length T- and B-cell repertoire sequencing
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0.2">migmap</requirement> 5 <requirement type="package" version="1.0.2">migmap</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors='exit_code'><![CDATA[ 7 <command detect_errors='exit_code'><![CDATA[
8 export IGBLAST_PATH=\$(dirname \$(which igblastn)) && 8 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
9 mkdir temp_db &&
10 ln -s "\${IGBLAST_PATH}/../share/igblast/" ./temp_db/ &&
11
9 #if $input.is_of_type('fasta') : 12 #if $input.is_of_type('fasta') :
10 ln -s '$input' in.fa && 13 ln -s '$input' in.fa &&
11 #else 14 #else
12 ln -s '$input' in.fq && 15 ln -s '$input' in.fq &&
13 #end if 16 #end if
20 $by_read 23 $by_read
21 #if str($qual_threshold): 24 #if str($qual_threshold):
22 -q $qual_threshold 25 -q $qual_threshold
23 #end if 26 #end if
24 -p "\${GALAXY_SLOTS:-4}" 27 -p "\${GALAXY_SLOTS:-4}"
25 --data-dir "\${IGBLAST_PATH}/../share/igblast" 28 --data-dir ./temp_db/igblast/
26 -S $species 29 -S $species
27 -R $receptor_list 30 -R $receptor_list
28 --report '$report'
29 #if $input.is_of_type('fasta'): 31 #if $input.is_of_type('fasta'):
30 in.fa 32 in.fa
31 #else 33 #else
32 in.fq 34 in.fq
33 #end if 35 #end if
69 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false' 71 <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
70 truevalue="--by-read" falsevalue=""/> 72 truevalue="--by-read" falsevalue=""/>
71 </inputs> 73 </inputs>
72 <outputs> 74 <outputs>
73 <data name="output" format="tabular"/> 75 <data name="output" format="tabular"/>
74 <data name="report" format="txt"/>
75 </outputs> 76 </outputs>
76 <tests> 77 <tests>
77 <test> 78 <test>
78 <param name="input" value="test_stop_codon.fa"/> 79 <param name="input" value="test_stop_codon.fa"/>
79 <param name="allow_noncoding" value="--allow-noncoding"/> 80 <param name="allow_noncoding" value="--allow-noncoding"/>