comparison chimera.slayer.xml @ 2:6f7f890e6a54 draft

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

1:1cce71e7e7ef

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

        ## enable mothur to find blast
        loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&

        ## create symlinks to input datasets
        ln -s "$fasta" fasta.dat &&
        #if $alignment.source == "self":
            ln -s "$alignment.name" alignment.name.dat &&
            ln -s "$alignment.group" alignment.group.dat &&
            ln -s "$alignment.count" alignment.count.dat &&
        #else:
            ln -s "$alignment.template" alignment.template.dat &&
        #end if

        echo 'chimera.slayer(
            fasta=fasta.dat,
            #if $alignment.source == "self":
                reference=self,
                #if $alignment.name:
                    name=$alignment.name,
                #end if
                #if $alignment.group:
                    group=$alignment.group,
                #end if
                #if $alignment.count:
                    count=$alignment.count,
                #end if
            #else:
                reference=$alignment.template,
            #end if
            #if $options.setby == "user":
                search=$options.search,
                window=$options.window,
                increment=$options.increment,
                match=$options.match,
                mismatch=$options.mismatch,
                numwanted=$options.numwanted,
                parents=$options.parents,
                minsim=$options.minsim,
                mincov=$options.mincov,
                iters=$options.iters,
                minbs=$options.minbs,
                minsnp=$options.minsnp,
                divergence=$options.divergence,
                trim=$options.trim,
                split=$options.split,
            #end if
            dereplicate=$dereplicate,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | ./mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
        <conditional name="alignment">
            <param name="source" type="select" label="Select Reference Template from" help="">
                <option value="hist">History</option>
                <option value="ref">Cached Reference</option>
                <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option>
            </param>
            <when value="ref">
                <param name="template" type="select" label="reference - Select an alignment database " help="">
                    <options from_data_table="mothur_aligndb">
                    </options>
                </param>
            </when>
            <when value="hist">
                <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
            </when>
            <when value="self">
                <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Count file"/>
                <param name="name" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/>
                <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference" help="use the more abundant sequences from the same sample to check the query sequence"/>
            </when>
        </conditional>
        <conditional name="options">
            <param name="setby" type="select" label="Slayer Options" help="">
                <option value="default">Use default settings</option>
                <option value="user">Manually set options</option>
            </param>
            <when value="default"/>
            <when value="user">
                <param name="search" type="select" label="search - Search method for finding the closest parent" help="">
                    <option value="blast" selected="true">blast</option>
                    <option value="kmer">kmer</option>
                </param>
                <param name="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)"/>
                <param name="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)"/>
                <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/>
                <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/>
                <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/>
                <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/>
                <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/>
                <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/>
                <param name="iters" type="integer" value="1000" label="iters - Number of bootstrap iterations to try (default 100)"/>
                <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/>
                <param name="minsnp" type="integer" value="10" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/>
                <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/>
                <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="trim - include chimeric sequences trimmed to their longest peice"/>
                <param name="split" type="boolean" truevalue="true" falsevalue="false" checked="false" label="split - detect tri- and quadmeras" help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/>
            </when>
        </conditional>
        <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_file" from_work_dir="fasta.slayer.chimeras" format="txt" label="${tool.name} on ${on_string}: slayer.chimeras"/>
        <data name="out_accnos" from_work_dir="fasta.slayer.accnos" format="mothur.accnos" label="${tool.name} on ${on_string}: slayer.accnos"/>
    </outputs>
    <tests>
        <test><!-- test with external reference -->
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <param name="source" value="hist"/>
            <param name="template" value="HMP_MOCK.v35.align"/>
            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras" ftype="txt"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with self as reference -->
            <param name="fasta" value="HMP_MOCK.v35.align"/>
            <param name="source" value="self"/>
            <param name="setby" value="user"/>
            <param name="search" value="kmer"/>
            <param name="name" value="HMP_MOCK.v35.align.names"/>
            <output name="out_file" file="HMP_MOCK.v35.slayer.chimeras" ftype="txt"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>

    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

.. _ChimeraSlayer: http://microbiomeutil.sourceforge.net/
.. _chimera.slayer: https://www.mothur.org/wiki/Chimera.slayer

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

2:6f7f890e6a54

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

## enable mothur to find blast
ln -s ln -s `dirname \$(which mothur)`/* . &&

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
#if $alignment.source == "self":
    ln -s '$alignment.name' alignment.name.dat &&
    ln -s '$alignment.group' alignment.group.dat &&
    ln -s '$alignment.count' alignment.count.dat &&
#else:
    ln -s '$alignment.reference' alignment.reference.dat &&
#end if

echo 'chimera.slayer(
    fasta=fasta.dat,
    #if $alignment.source == "self":
        reference=self,
        #if $alignment.name:
            name=$alignment.name,
        #end if
        #if $alignment.group:
            group=$alignment.group,
        #end if
        #if $alignment.count:
            count=$alignment.count,
        #end if
    #else:
        reference=$alignment.reference,
    #end if
    #if $options.setby == "user":
        search=$options.search,
        window=$options.window,
        increment=$options.increment,
        match=$options.match,
        mismatch=$options.mismatch,
        numwanted=$options.numwanted,
        parents=$options.parents,
        minsim=$options.minsim,
        mincov=$options.mincov,
        iters=$options.iters,
        minbs=$options.minbs,
        minsnp=$options.minsnp,
        divergence=$options.divergence,
        trim=$options.trim,
        split=$options.split,
    #end if
    dereplicate=$dereplicate,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| ./mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
        <conditional name="alignment">
            <param name="source" type="select" label="Select Reference Template from">
                <option value="hist">History</option>
                <option value="ref">Cached Reference</option>
                <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option>
            </param>
            <when value="ref">
                <param argument="reference" type="select" label="reference - Select an alignment database">
                    <options from_data_table="mothur_aligndb">
                    </options>
                </param>
            </when>
            <when value="hist">
                <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
            </when>
            <when value="self">
                <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count file"/>
                <param argument="name" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/>
                <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
                    help="use the more abundant sequences from the same sample to check the query sequence"/>
            </when>
        </conditional>
        <conditional name="options">
            <param name="setby" type="select" label="Slayer Options">
                <option value="default">Use default settings</option>
                <option value="user">Manually set options</option>
            </param>
            <when value="default"/>
            <when value="user">
                <param argument="search" type="select" label="search - Search method for finding the closest parent">
                    <option value="blast" selected="true">blast</option>
                    <option value="kmer">kmer</option>
                </param>
                <param argument="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)"/>
                <param argument="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)"/>
                <param argument="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/>
                <param argument="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/>
                <param argument="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/>
                <param argument="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/>
                <param argument="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/>
                <param argument="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/>
                <param argument="iters" type="integer" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/>
                <param argument="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/>
                <param argument="minsnp" type="integer" value="10" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 10)"/>
                <param argument="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/>
                <param argument="trim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="trim - include chimeric sequences trimmed to their longest piece"/>
                <param argument="split" type="boolean" truevalue="true" falsevalue="false" checked="false" label="split - detect tri- and quadmeras"
                    help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/>
            </when>
        </conditional>
        <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups"
            help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="slayer.chimeras" from_work_dir="fasta.slayer.chimeras" format="txt" label="${tool.name} on ${on_string}: slayer.chimeras"/>
        <data name="out_accnos" from_work_dir="fasta.slayer.accnos" format="mothur.accnos" label="${tool.name} on ${on_string}: slayer.accnos"/>
    </outputs>
    <tests>
        <test><!-- test with external reference -->
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <param name="source" value="hist"/>
            <param name="reference" value="HMP_MOCK.v35.align"/>
            <output name="slayer.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras" ftype="txt"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with self as reference -->
            <param name="fasta" value="HMP_MOCK.v35.align"/>
            <param name="source" value="self"/>
            <param name="setby" value="user"/>
            <param name="search" value="kmer"/>
            <param name="name" value="HMP_MOCK.v35.align.names"/>
            <output name="slayer.chimeras" file="HMP_MOCK.v35.slayer.chimeras" ftype="txt"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

.. _ChimeraSlayer: http://microbiomeutil.sourceforge.net/
.. _chimera.slayer: https://www.mothur.org/wiki/Chimera.slayer

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