comparison trim.flows.xml @ 2:9d48c9a47566 draft

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

1:d40f783c5d65

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

        ## create symlinks to input datasets
        ln -s "$flow" flow.dat &&
        #if $oligo.add == "yes":
            ln -s "$oligo.oligos" oligo.oligos.dat &&
        #end if

        echo 'trim.flows(
            flow=flow.dat,
            minflows=$minflows,
            maxflows=$maxflows,
            #if $maxhomop:
                maxhomop=$maxhomop,
            #end if
            order=$order,
            signal=$signal,
            noise=$noise,
            #if $oligo.add == "yes":
                oligos=oligo.oligos.dat,
                bdiffs=$oligo.bdiffs,
                pdiffs=$oligo.pdiffs,
                tdiffs=$oligo.tdiffs,
                ldiffs=$oligo.ldiffs,
                sdiffs=$oligo.sdiffs,
            #end if
            fasta=$fasta,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
        ## prevent these two files from being gathered into collection
        && mv flow.trim.flow flow.trim
        && mv flow.scrap.flow flow.scrap
    ]]></command>
    <inputs>
        <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file"/>
        <conditional name="oligo">
            <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file">

            <option value="A" selected="true"> A (TACG) </option>
            <option value="B"> B </option>
            <option value="I"> I </option>
        </param>
        <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="trim_flow" format="mothur.sff.flow" from_work_dir="flow.trim" label="${tool.name} on ${on_string}: trim.flow"/>
        <data name="scrap_flow" format="mothur.sff.flow" from_work_dir="flow.scrap" label="${tool.name} on ${on_string}: scrap.flow"/>

            <output name="flow_files" ftype="tabular">
                <assert_contents>
                    <has_text text="flow"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos file and fasta output -->
            <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
            <param name="add" value="yes"/>

            </output>
            <output_collection name="flow_oligos" count="2">
                <element name="F003D006" md5="5ea6613d7aa26f87ca9b983152e14a4b" ftype="mothur.sff.flow"/>
            </output_collection>
            <output name="flow_fasta" md5="0725967a9ed731c049d48ea876b0e308" ftype="fasta"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers.

.. _trim.flows: https://www.mothur.org/wiki/Trim.flows

]]>
    </help>
    <expand macro="citations"/>
</tool>

2:9d48c9a47566

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

## create symlinks to input datasets
ln -s '$flow' flow.dat &&
#if $oligo.add == "yes":
    ln -s '$oligo.oligos' oligo.oligos.dat &&
#end if

echo 'trim.flows(
    flow=flow.dat,
    minflows=$minflows,
    maxflows=$maxflows,
    #if $maxhomop:
        maxhomop=$maxhomop,
    #end if
    order=$order,
    signal=$signal,
    noise=$noise,
    #if $oligo.add == "yes":
        oligos=oligo.oligos.dat,
        bdiffs=$oligo.bdiffs,
        pdiffs=$oligo.pdiffs,
        tdiffs=$oligo.tdiffs,
        ldiffs=$oligo.ldiffs,
        sdiffs=$oligo.sdiffs,
    #end if
    fasta=$fasta,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log

## prevent these two files from being gathered into collection
&& mv flow.trim.flow flow.trim
&& mv flow.scrap.flow flow.scrap
    ]]></command>
    <inputs>
        <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file"/>
        <conditional name="oligo">
            <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file">

            <option value="A" selected="true"> A (TACG) </option>
            <option value="B"> B </option>
            <option value="I"> I </option>
        </param>
        <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="trim_flow" format="mothur.sff.flow" from_work_dir="flow.trim" label="${tool.name} on ${on_string}: trim.flow"/>
        <data name="scrap_flow" format="mothur.sff.flow" from_work_dir="flow.scrap" label="${tool.name} on ${on_string}: scrap.flow"/>

            <output name="flow_files" ftype="tabular">
                <assert_contents>
                    <has_text text="flow"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos file and fasta output -->
            <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
            <param name="add" value="yes"/>

            </output>
            <output_collection name="flow_oligos" count="2">
                <element name="F003D006" md5="5ea6613d7aa26f87ca9b983152e14a4b" ftype="mothur.sff.flow"/>
            </output_collection>
            <output name="flow_fasta" md5="0725967a9ed731c049d48ea876b0e308" ftype="fasta"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers.

.. _trim.flows: https://www.mothur.org/wiki/Trim.flows

    ]]></help>
    <expand macro="citations"/>
</tool>