comparison crossmap_vcf.xml @ 9:30d4d3bbe0a1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 07b2b6b9b288fd4ad368fc7a4f0143bb73e9edd9"

8:4a9c59111f54

    <expand macro="version_command"/>

    <command detect_errors="aggressive"><![CDATA[
#set $input_file = str($seq_source.input)

CrossMap.py vcf

#if $seq_source.index_source_s == "cached"
    ## This is the 2nd dbkey, and the corresponding value has to be looked up
    "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
#else
    '${seq_source.chain_source.input_chain}'
#end if

'${input_file}'
'${seq_source.input_fasta}'
$no_comp_alleles
output
    ]]></command>

    <inputs>

9:30d4d3bbe0a1

    <expand macro="version_command"/>

    <command detect_errors="aggressive"><![CDATA[
#set $input_file = str($seq_source.input)

ln -s '${seq_source.input_fasta}' 'genome.fasta' &&

CrossMap.py vcf

#if $seq_source.index_source_s == "cached"
    ## This is the 2nd dbkey, and the corresponding value has to be looked up
    "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
#else
    '${seq_source.chain_source.input_chain}'
#end if

'${input_file}'
'genome.fasta'
$no_comp_alleles
output
    ]]></command>

    <inputs>