comparison stacks_genotypes.xml @ 3:aa333a0a7d5a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

2:dbe3901aace2

<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0">
    <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        mkdir stacks_outputs

        &&

        #for $input_file in $input_col:
            #set $ext = ""
            #if not str($input_file.name).endswith('.tsv'):
                #set $ext = ".tsv"
            #end if
            ln -s "${input_file}" "stacks_outputs/${input_file.name}${ext}" &&
        #end for

        genotypes

            -P stacks_outputs

3:aa333a0a7d5a

<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.1">
    <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        #import re

        mkdir stacks_outputs

        &&

        #for $input_file in $input_col:
            #set $filename = str($input_file.element_identifier)
            #if not $filename.endswith('.tsv'):
                #set $filename = $filename + ".tsv"
            #end if
            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename):
                ln -s "${input_file}" "stacks_outputs/${filename}" &&
            #end if
        #end for

        genotypes

            -P stacks_outputs