comparison make.sra.xml @ 2:82e91bb188b2 draft

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

1:d21f004a8e1d

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

        ## create symlinks to input datasets
        ln -s "$project" project.dat &&
        ln -s "$sff" sff.dat &&
        ln -s "$oligos" oligos.dat &&
        ln -s "$mimark" mimark.dat &&
        ln -s "$fastq" fastq.dat &&

        echo 'make.sra(
            project=project.dat,
            sff=sff.dat,
            oligos=oligos.dat,
            mimark=mimark.dat,
            #if $fastq:
                fastq=fastq.dat,
            #end if
            bdiffs=$bdiffs,
            pdiffs=$pdiffs,
            tdiffs=$tdiffs,
            ldiffs=$ldiffs,
            sdiffs=$sdiffs,
            checkorient=$checkorient,
            orientation=$orientation,
            platform=$platform,
            instrument=$instrument,
            libstrategy=$libstrategy,
            libselection=$libselection,
            libsource=$libsource,
            datatype=$datatype
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="project" type="data" format="tabular" label="Project file"/>
        <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
        <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>

            <option value="EPIGENOMICS">EPIGENOMICS</option>
            <option value="PHENOTYPE">PHENOTYPE</option>
            <option value="GENOTYPE">GENOTYPE</option>
            <option value="OTHER">OTHER</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
        <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>

                    <has_text text="Submission"/>
                    <has_text text="Attribute"/>
                    <has_text text="BioProject"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The make.sra_ creates the necessary files for a NCBI submission.

.. _make.sra: https://www.mothur.org/wiki/Make.sra

]]>
    </help>
    <citations>
        <citation type="doi">10.1128/AEM.01541-09</citation>
    </citations>
</tool>

2:82e91bb188b2

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

## create symlinks to input datasets
ln -s '$project' project.dat &&
ln -s '$sff' sff.dat &&
ln -s '$oligos' oligos.dat &&
ln -s '$mimark' mimark.dat &&
ln -s '$fastq' fastq.dat &&

echo 'make.sra(
    project=project.dat,
    sff=sff.dat,
    oligos=oligos.dat,
    mimark=mimark.dat,
    #if $fastq:
        fastq=fastq.dat,
    #end if
    bdiffs=$bdiffs,
    pdiffs=$pdiffs,
    tdiffs=$tdiffs,
    ldiffs=$ldiffs,
    sdiffs=$sdiffs,
    checkorient=$checkorient,
    orientation=$orientation,
    platform=$platform,
    instrument=$instrument,
    libstrategy=$libstrategy,
    libselection=$libselection,
    libsource=$libsource,
    datatype=$datatype,
    trim=$trim,
    includescrap=$includescrap
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="project" type="data" format="tabular" label="Project file"/>
        <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
        <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>

            <option value="EPIGENOMICS">EPIGENOMICS</option>
            <option value="PHENOTYPE">PHENOTYPE</option>
            <option value="GENOTYPE">GENOTYPE</option>
            <option value="OTHER">OTHER</option>
        </param>
        <param name="trim" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Trim sequences and quality scores?" help="will trim to the clipQualLeft and clipQualRight values in sff file"/>
        <param name="includescrap" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Include scrapped sequences in your submission?"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
        <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>

                    <has_text text="Submission"/>
                    <has_text text="Attribute"/>
                    <has_text text="BioProject"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The make.sra_ creates the necessary files for a NCBI submission.

.. _make.sra: https://www.mothur.org/wiki/Make.sra

    ]]></help>
    <citations>
        <citation type="doi">10.1128/AEM.01541-09</citation>
    </citations>
</tool>