Mercurial > repos > iuc > crossmap_vcf

comparison crossmap_vcf.xml @ 8:6e96c77f5824 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 07b2b6b9b288fd4ad368fc7a4f0143bb73e9edd9"
author iuc
date Tue, 16 Nov 2021 19:16:46 +0000
parents 71730c177cdf
children d4965adac10c
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7:71730c177cdf 8:6e96c77f5824
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 9
10 <command detect_errors="aggressive"><![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 ln -s '${seq_source.input_fasta}' 'genome.fasta' &&
14
13 CrossMap.py vcf 15 CrossMap.py vcf
14 16
15 #if $seq_source.index_source_s == "cached" 17 #if $seq_source.index_source_s == "cached"
16 ## This is the 2nd dbkey, and the corresponding value has to be looked up 18 ## This is the 2nd dbkey, and the corresponding value has to be looked up
17 "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" 19 "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
18 #else 20 #else
19 '${seq_source.chain_source.input_chain}' 21 '${seq_source.chain_source.input_chain}'
20 #end if 22 #end if
21 23
22 '${input_file}' 24 '${input_file}'
23 '${seq_source.input_fasta}' 25 'genome.fasta'
24 $no_comp_alleles 26 $no_comp_alleles
25 output 27 output
26 ]]></command> 28 ]]></command>
27 29
28 <inputs> 30 <inputs>