comparison abromics_galaxy_json_extractor.xml @ 3:1861b7f49aed draft

planemo upload for repository https://gitlab.com/ifb-elixirfr/abromics/galaxy-tools commit 12dee18b8a3e5f84bb774bc170895cd3245c57d0

2:857426567aca

        | tee "$logfile"
        #if $i < $counter
            &&
        #end if
    #end for
        && ls abromics_extracted_folder
        ]]>
    </command>
    <inputs>
        <section name="tool_section" title="Available tools" expanded="true">
            <repeat name="tools" title="Tool" min="0">

        | Quast          | 5.2.0          |  output.tsv       |                                                            |
        | Recentrifuge   | 1.10.0         |  data.tsv         | report.html, stat.tsv                                      |
        | Refseqmasher   | 0.1.2          |  output.tsv       |                                                            |
        | Shovill        | 1.1.0          |  contigs.fasta    | alignment.bam, contigs.gfa                                 |
        | Staramr        | 0.9.1          |  resfinder.tsv    | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |
        | tabular_file   |  0             |    output.tsv     | no optional files                                          |

        ** Options **
        You can add a tool version and a database version for related tools.
        For some tools you can add optional files previously produced by the tool
            ]]></help>

3:1861b7f49aed

        | tee "$logfile"
        #if $i < $counter
            &&
        #end if
    #end for
        ]]>
    </command>
    <inputs>
        <section name="tool_section" title="Available tools" expanded="true">
            <repeat name="tools" title="Tool" min="0">

        | Quast          | 5.2.0          |  output.tsv       |                                                            |
        | Recentrifuge   | 1.10.0         |  data.tsv         | report.html, stat.tsv                                      |
        | Refseqmasher   | 0.1.2          |  output.tsv       |                                                            |
        | Shovill        | 1.1.0          |  contigs.fasta    | alignment.bam, contigs.gfa                                 |
        | Staramr        | 0.9.1          |  resfinder.tsv    | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |
        | tabular_file   |  0             |  output.tsv       | no optional files                                          |

        ** Options **
        You can add a tool version and a database version for related tools.
        For some tools you can add optional files previously produced by the tool
            ]]></help>