comparison roary.xml @ 8:e88a7de55d6e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit fde1985c9d6860f9a03ddfd38378a5c3f5e31fcb"

7:78608ec02d62

<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
    <macros>
        <token name="@TOOL_VERSION@">3.13.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        #set $filenames = list()
        #for $gff in $gff_input.gffs
            cp '$gff' '${gff.element_identifier}.gff' &&
            #set $filename = str($gff.element_identifier) + '.gff'
            $filenames.append(str($filename))
        #end for

        roary
          -f out

8:e88a7de55d6e

<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
    <xrefs>
        <xref type="bio.tools">roary</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">3.13.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set $filenames = list()
        #for $gff in $gff_input.gffs
            #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($gff.element_identifier))
            ln -s '$gff' '${escaped_element_identifier}.gff' &&
            #set $filename = str($escaped_element_identifier) + '.gff'
            $filenames.append(str($filename))
        #end for

        roary
          -f out