comparison degap.seqs.xml @ 2:f643cbd3a967 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

1:bd09ab148632

    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @SHELL_OPTIONS@

        ## create symlinks to input datasets
        ln -s "$fasta" fasta.dat &&

        echo 'degap.seqs(
            fasta=fasta.dat
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

2:f643cbd3a967

    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&

echo 'degap.seqs(
    fasta=fasta.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[