Mercurial > repos > iuc > crossmap_vcf

comparison crossmap_vcf.xml @ 4:9d61d74f03a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
author iuc
date Wed, 11 Sep 2019 19:29:21 -0400
parents 9db73ff23c9f
children 71730c177cdf
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3:9db73ff23c9f 4:9d61d74f03a4
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 9
10 <command><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 #set $input_file = str($seq_source.input) 11 #set $input_file = str($seq_source.input)
12 12
13 CrossMap.py vcf 13 CrossMap.py vcf
14 14
15 #if $seq_source.index_source_s == "cached" 15 #if $seq_source.index_source_s == "cached"
75 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/> 75 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/>
76 <has_text text="##new_reference_genome="/> 76 <has_text text="##new_reference_genome="/>
77 <has_text text="#CHROM"/> 77 <has_text text="#CHROM"/>
78 <has_text_matching expression="2.*?rs11449.*?PASS"/> 78 <has_text_matching expression="2.*?rs11449.*?PASS"/>
79 <has_text_matching expression="2.*?rs84825.*?PASS"/> 79 <has_text_matching expression="2.*?rs84825.*?PASS"/>
80 <has_text_matching expression="2.*?rs84823.*?PASS"/>
81 </assert_contents> 80 </assert_contents>
82 </output> 81 </output>
83 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/> 82 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
84 </test> 83 </test>
85 </tests> 84 </tests>