comparison racon.xml @ 8:e100a765370e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f

7:39bed8de8017

<tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>racon --version</version_command>

            #else:
                overlaps.paf
            #end if
            corrected_reads.$cext
            -t \${GALAXY_SLOTS:-4} 
            $u
            $f
            -w $w
            -q $q
            -e $e
            -m $m
            -x $x
            -g $g
            > racon_polished_consensus.fa  
    ]]></command>
    <inputs>
        <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/>
        <param type="data" name="overlaps" format="paf,sam,tabular" label="Overlaps"/>
        <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/>

        <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" />
        <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" />
        <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" />
        <param argument="-q" type="float" value="10.0" label="Threshold for average base quality of windows used in poa" />
        <param argument="-e" type="float" value="0.3" label="Maximum allowed error rate used for filtering overlaps" />
        <param argument="-m" type="integer" value="5" label="Score for matching bases" />
        <param argument="-x" type="integer" value="-4" label="Score for mismatching bases" />
        <param argument="-g" type="integer" value="-8" max="0" label="Gap penalty" />        
        
    </inputs>
    <outputs>
        <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" />
    </outputs>
    <tests>
        <test>
            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
            <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
            <param name="u" value="true"/>
            <param name="f" value="true"/>
            <param name="w" value="800"/>
            <param name="e" value="0.2"/>
            <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
        </test>
        <test>
            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
            <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
            <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

8:e100a765370e

<tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Consensus module for raw de novo DNA assembly of long uncorrected reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>racon --version</version_command>

            #else:
                overlaps.paf
            #end if
            corrected_reads.$cext
            -t \${GALAXY_SLOTS:-4} 
            $include_unpolished
            $fragment_correction
            -w $window_length
            -q $quality_threshold
            -e $error_threshold
            $no_trimming
            -m $match
            -x $mismatch
            -g $gap
            > racon_polished_consensus.fa  
    ]]></command>
    <inputs>
        <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences" help="input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences used for correction"/>
        <param type="data" name="overlaps" format="paf,sam,tabular" label="Overlaps" help="input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences"/>
        <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences" help="Input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be corrected"/>
        <param argument="--include-unpolished" type="boolean" truevalue="-u" falsevalue="" label="Include unpolished" help="Output unpolished target sequences" />
        <param argument="--fragment-correction" type="boolean" truevalue="-f" falsevalue="" label="Fragment correction" help="Perform fragment correction instead of contig polishing. Note: overlaps file should contain dual/self overlaps" />
        <param argument="--window-length" type="integer" value="500" label="Window length" help="Size of window on which POA is performed"/>
        <param argument="--quality-threshold" type="float" min="0" value="10.0" label="Quality threshold" help="Threshold for average base quality of windows used in POA"/>
        <param argument="--error-threshold" type="float" min="0" value="0.3" label="Error threshold" help="Maximum allowed error rate used for filtering overlaps" />
        <param argument="--no-trimming" type="boolean" truevalue="--no-trimming" falsevalue="" checked="false" label="No trimming" help="Disables consensus trimming at window ends" />
        <param argument="--match" type="integer" value="3" label="Match score" help="Score for matching bases. Defalt: 3" />
        <param argument="--mismatch" type="integer" value="-5" label="Mismatch score" help="Score for mismatching bases. Default: -5" />
        <param argument="--gap" type="integer" value="-4" max="0" label="Gap penalty" />        
    </inputs>
    <outputs>
        <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" label="${tool.name} on ${on_string}: consensus sequence"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
            <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
            <param name="include_unpolished" value="true"/>
            <param name="fragment_correction" value="true"/>
            <param name="window_length" value="800"/>
            <param name="error_threshold" value="0.2"/>
            <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
            <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
            <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
            <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
            <param name="include_unpolished" value="false"/>
            <param name="fragment_correction" value="false"/>
            <param name="quality_threshold" value="9.0"/>
            <param name="no_trimming" value="true"/>
            <param name="match" value="7"/>
            <param name="mismatch" value="-4"/>
            <param name="gap" value="-3"/>
            <output name="consensus" ftype="fasta" file="consensus_result1.fasta"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**