comparison maxbin2.xml @ 3:cfd50144a871 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"

2:6a638de7915c

<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy1">
    <description>clusters metagenomic contigs into bins</description>
    <macros>
        <token name="@MAXBIN_VERSION@">2.2.7</token>
    </macros>
    <requirements>

        $adv_cond.plotmarker
        -markerset $adv_cond.markerset
    #end if
    -thread \${GALAXY_SLOTS:-1}

    && tar -xf out.marker_of_each_bin.tar.gz

	## redirect the idba out and err file content to stdout and err
	## since this is also wanted in case the error case ';' is used here to 
	## separate commands
    #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
        ; echo "==== IDBA stdout ===="
        && cat out.idba.out
        && echo "==== IDBA stderr ====" 1>&2
        && cat out.idba.err 1>&2
    #end if
    ]]></command>
    <inputs>
        <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
          <conditional name="intype_cond">

        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4"><!-- test w contigs and reads as input -->
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="intype_cond">
                <param name="intype_select" value="rds"/>
                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
            </conditional>

3:cfd50144a871

<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2">
    <description>clusters metagenomic contigs into bins</description>
    <macros>
        <token name="@MAXBIN_VERSION@">2.2.7</token>
    </macros>
    <requirements>

        $adv_cond.plotmarker
        -markerset $adv_cond.markerset
    #end if
    -thread \${GALAXY_SLOTS:-1}

    && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -

    ## redirect the idba out and err file content to stdout and err
    ## since this is also wanted in case the error case ';' is used here to 
    ## separate commands
    #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
        ; echo "==== IDBA stdout ===="
        && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
        && echo "==== IDBA stderr ====" 1>&2
        && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
    #end if
    ]]></command>
    <inputs>
        <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
          <conditional name="intype_cond">

        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </data>
    </outputs>
    <tests>
        <!-- test w contigs and reads as input -->
        <test expect_num_outputs="4">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="intype_cond">
                <param name="intype_select" value="rds"/>
                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
            </conditional>