comparison seq.error.xml @ 2:a5418319c97a draft

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

1:29fa3670faa5

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

        ## create symlinks to input datasets
        ln -s "$fasta_in" fasta_in.dat &&
        ln -s "$name_in" name_in.dat &&
        ln -s "$count" count.dat &&
        ln -s "$alignment.template" alignment.template.dat &&
        #if $qual.use == "yes":
            ln -s "$qual.qfile_in" qfile_in.dat &&
            ln -s "$qual.alignreport_in" alignreport_in.dat &&
        #end if

        echo 'seq.error(
            fasta=fasta_in.dat,
            reference=alignment.template.dat,
            #if $name_in:
                name=name_in.dat,
            #end if
            #if $qual.use == "yes":
                qfile=qfile_in.dat,
                report=alignreport_in.dat,
            #end if
            #if $threshold:
                threshold=$threshold,
            #end if
            ignorechimeras=$ignorechimeras,
            #if $count:
                count=count.dat,
            #end if
            #if $fasta_in.is_of_type('mothur.align')
                aligned=T,
            #else
                aligned=F,
            #end if
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
        <conditional name="alignment">
            <param name="source" type="select" label="Select Reference Template from" help="">

            <when value="no"/>
        </conditional>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
        <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
        <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
            <filter>'summary' in output_sel</filter>

            <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
            <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
            <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
            <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
            <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!--test with qual file and all outputs -->
            <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
            <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>

            <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
            <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
            <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
            <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
            <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis

.. _template_alignment: https://www.mothur.org/wiki/Alignment_database
.. _seq.error: https://www.mothur.org/wiki/Seq.error

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

2:a5418319c97a

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

## create symlinks to input datasets
ln -s '$fasta_in' fasta_in.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$count' count.dat &&
ln -s '$alignment.template' alignment.template.dat &&
#if $qual.use == "yes":
    ln -s '$qual.qfile_in' qfile_in.dat &&
    ln -s '$qual.alignreport_in' alignreport_in.dat &&
#end if

echo 'seq.error(
    fasta=fasta_in.dat,
    reference=alignment.template.dat,
    #if $name_in:
        name=name_in.dat,
    #end if
    #if $qual.use == "yes":
        qfile=qfile_in.dat,
        report=alignreport_in.dat,
    #end if
    #if $threshold:
        threshold=$threshold,
    #end if
    ignorechimeras=$ignorechimeras,
    #if $count:
        count=count.dat,
    #end if
    #if $fasta_in.is_of_type('mothur.align')
        aligned=T,
    #else
        aligned=F,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
        <conditional name="alignment">
            <param name="source" type="select" label="Select Reference Template from" help="">

            <when value="no"/>
        </conditional>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
        <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
        <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
            <filter>'summary' in output_sel</filter>

            <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
            <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
            <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
            <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
            <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!--test with qual file and all outputs -->
            <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
            <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>

            <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
            <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
            <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
            <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
            <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis

.. _template_alignment: https://www.mothur.org/wiki/Alignment_database
.. _seq.error: https://www.mothur.org/wiki/Seq.error

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