comparison trim.seqs.xml @ 2:baa3df51e2b7 draft

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

1:de357ac9db36

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

        ## create symlinks to input datasets
        ln -s "$fasta" fasta.dat &&
        ln -s "$names" names.dat &&
        ln -s "$count" count.dat &&
        #if $oligo.add == "yes":
            ln -s "$oligo.oligos" oligo.oligos.dat &&
        #end if
        #if $qual.add2 == "yes":
            ln -s "$qual.qfile" qual.qfile.dat &&
        #end if

        echo 'trim.seqs(
            fasta=fasta.dat,
            minlength=$minlength,
            maxlength=$maxlength,
            maxambig=$maxambig,
            maxhomop=$maxhomop,
            keepfirst=$keepfirst,
            removelast=$removelast,
            #if $oligo.add == "yes":
                oligos=oligo.oligos.dat,
                bdiffs=$oligo.bdiffs,
                pdiffs=$oligo.pdiffs,
                tdiffs=$oligo.tdiffs,
                ldiffs=$oligo.ldiffs,
                sdiffs=$oligo.sdiffs,
                keepforward=$oligo.keepforward,
                allfiles=$oligo.allfiles,
            #end if
            #if $qual.add2 == "yes":
                qfile=qual.qfile.dat,
                qaverage=$qual.qaverage,
                qthreshold=$qual.qthreshold,
                qwindowaverage=$qual.qwindowaverage,
                qwindowsize=$qual.qwindowsize,
                rollaverage=$qual.rollaverage,
                qstepsize=$qual.qstepsize,
                qtrim=$qual.qtrim,
            #end if
            flip=$flip,
            #if $names:
                name=names.dat,
            #end if
            logtransform=$logtransform,
            checkorient=$checkorient,
            #if $count:
                count=count.dat,
            #end if
            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 fasta.trim.fasta fasta.trim
        && mv fasta.scrap.fasta fasta.scrap
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
        <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
        <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>

        </conditional>
        <param name="flip" type="boolean" truevalue="true" falsevalue="false" checked="false" label="flip - reverse complement the trimmed sequences"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
        <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
        <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/>
        <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/>

            <param name="maxhomop" value="4"/>
            <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
            <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
            <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
            <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with count table -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
            <param name="maxhomop" value="4"/>
            <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
            <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
            <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
            <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="add" value="yes"/>

            <param name="bdiffs" value="100"/>
            <param name="pdiffs" value="100"/>
            <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
            <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
            <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos and allfiles parameter -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="add" value="yes"/>

                <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/>
            </output_collection>
            <output_collection name="fasta_allfiles" count="9">
                <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with qfile-->
            <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/>
            <param name="add2" value="yes"/>

            <param name="maxhomop" value="4"/>
            <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/>
            <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
            <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
            <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences.  The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.

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

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

2:baa3df51e2b7

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

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$names' names.dat &&
ln -s '$count' count.dat &&
#if $oligo.add == "yes":
    ln -s '$oligo.oligos' oligo.oligos.dat &&
#end if
#if $qual.add2 == "yes":
    ln -s '$qual.qfile' qual.qfile.dat &&
#end if

echo 'trim.seqs(
    fasta=fasta.dat,
    minlength=$minlength,
    maxlength=$maxlength,
    maxambig=$maxambig,
    maxhomop=$maxhomop,
    keepfirst=$keepfirst,
    removelast=$removelast,
    #if $oligo.add == "yes":
        oligos=oligo.oligos.dat,
        bdiffs=$oligo.bdiffs,
        pdiffs=$oligo.pdiffs,
        tdiffs=$oligo.tdiffs,
        ldiffs=$oligo.ldiffs,
        sdiffs=$oligo.sdiffs,
        keepforward=$oligo.keepforward,
        allfiles=$oligo.allfiles,
    #end if
    #if $qual.add2 == "yes":
        qfile=qual.qfile.dat,
        qaverage=$qual.qaverage,
        qthreshold=$qual.qthreshold,
        qwindowaverage=$qual.qwindowaverage,
        qwindowsize=$qual.qwindowsize,
        rollaverage=$qual.rollaverage,
        qstepsize=$qual.qstepsize,
        qtrim=$qual.qtrim,
    #end if
    flip=$flip,
    #if $names:
        name=names.dat,
    #end if
    logtransform=$logtransform,
    checkorient=$checkorient,
    #if $count:
        count=count.dat,
    #end if
    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 fasta.trim.fasta fasta.trim
&& mv fasta.scrap.fasta fasta.scrap
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
        <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
        <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>

        </conditional>
        <param name="flip" type="boolean" truevalue="true" falsevalue="false" checked="false" label="flip - reverse complement the trimmed sequences"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
        <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
        <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/>
        <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/>

            <param name="maxhomop" value="4"/>
            <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
            <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
            <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
            <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with count table -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
            <param name="maxhomop" value="4"/>
            <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
            <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
            <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
            <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="add" value="yes"/>

            <param name="bdiffs" value="100"/>
            <param name="pdiffs" value="100"/>
            <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
            <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
            <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos and allfiles parameter -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="add" value="yes"/>

                <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/>
            </output_collection>
            <output_collection name="fasta_allfiles" count="9">
                <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with qfile-->
            <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/>
            <param name="add2" value="yes"/>

            <param name="maxhomop" value="4"/>
            <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/>
            <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
            <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
            <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences.  The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.

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

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