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comparison 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
comparison
equal deleted inserted replaced
4:1c8b286f8c13 5:862d0b2c3731
1 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
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 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">1.0.3</token> 5 <token name="@TOOL_VERSION@">1.0.3</token>
6 </macros> 6 </macros>
14 ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast && 14 ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
15 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast && 15 ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
16 16
17 #if $input.is_of_type('fasta') : 17 #if $input.is_of_type('fasta') :
18 ln -s '$input' in.fa && 18 ln -s '$input' in.fa &&
19 #else 19 #else if $input.is_of_type('fasta.gz') :
20 ln -s '$input' in.fa.gz &&
21 #else if $input.is_of_type('fastq') :
20 ln -s '$input' in.fq && 22 ln -s '$input' in.fq &&
23 #else if $input.is_of_type('fastq.gz') :
24 ln -s '$input' in.fq.gz
21 #end if 25 #end if
26
22 migmap 27 migmap
23 $allow_incomplete 28 $allow_incomplete
24 $allow_no_cdr3 29 $allow_no_cdr3
25 $allow_noncanonical 30 $allow_noncanonical
26 $allow_noncoding 31 $allow_noncoding
89 <param name="allow_incomplete" value="--allow-incomplete"/> 94 <param name="allow_incomplete" value="--allow-incomplete"/>
90 <param name="all_alleles" value="--all-alleles"/> 95 <param name="all_alleles" value="--all-alleles"/>
91 <output name="output" file="test_stop_codon.out"/> 96 <output name="output" file="test_stop_codon.out"/>
92 </test> 97 </test>
93 <test> 98 <test>
99 <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
100 <param name="allow_noncoding" value="--allow-noncoding"/>
101 <param name="by_read" value="--by-read"/>
102 <param name="allow_noncanonical" value="--allow-noncanonical"/>
103 <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
104 <param name="allow_incomplete" value="--allow-incomplete"/>
105 <param name="all_alleles" value="--all-alleles"/>
106 <output name="output" file="test_stop_codon.out" lines_diff="2"/>
107 </test>
108 <test>
94 <param name="allow_noncoding" value="--allow-noncoding"/> 109 <param name="allow_noncoding" value="--allow-noncoding"/>
95 <param name="by_read" value="--by-read"/> 110 <param name="by_read" value="--by-read"/>
96 <param name="input" value="test_out_of_frame.fa"/> 111 <param name="input" value="test_out_of_frame.fa"/>
97 <output name="output" file="test_out_of_frame.out"/> 112 <output name="output" file="test_out_of_frame.out"/>
98 </test> 113 </test>