view pear.xml @ 0:581e52f03c5d draft

Imported from capsule None

<tool id="iuc_pear" name="Pear" version="0.9.6.0">
    <description>Paired-End read merger</description>
    <!--<version_command>bismark version</version_command>-->
    <requirements>
        <requirement type="package" version="0.9.6">pear</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
<![CDATA[
    pear
        #if str( $library.type ) == "paired":
            -f "$library.forward"
            -r "$library.reverse"
        #else
            ## prepare collection
            -f $library.input_collection.forward
            -r $library.input_collection.reverse
        #end if

        --output pear
        --p-value $pvalue
        --min-overlap $min_overlap
        #if int($max_assembly_length) > 0:
            --max-asm-length $max_assembly_length
        #end if
        --min-asm-length $min_assembly_length
        --min-trim-length $min_trim_length
        --quality-theshold $quality_threshold
        --max-uncalled-base $max_uncalled_base
        --test-method $test_method
        --empirical-freqs $empirical_freqs
        -j "\${GALAXY_SLOTS:-8}"
        --score-method $score_method
        --cap $cap
        $nbase
]]>
    </command>
    <inputs>
        <conditional name="library">
            <param name="type" type="select" label="Dataset type">
              <option value="paired">Paired-end</option>
              <option value="paired_collection">Paired-end Dataset Collection</option>
            </param>
            <when value="paired">
                <param name="forward" type="data" format="fastqillumina, fastqsanger, fastq"
                    label="Name of file that contains the forward paired-end reads" help="-f" />
                <param name="reverse" type="data" format="fastqillumina, fastqsanger, fastq"
                    label="Name of file that contains the reverse paired-end reads" help="-r" />
            </when>
            <when value="paired_collection">
                <param name="input_collection" format="fastqillumina, fastqsanger, fastq"
                    type="data_collection" collection_type="paired"
                    label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33. (-f and -r)" />
            </when>
        </conditional>

        <!-- optional -->
        <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test"
            help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)" />

        <param name="min_overlap" type="integer" value="10" optional="True" label="Minimum overlap size"
            help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)" />

        <param name="max_assembly_length" type="integer" value="0" optional="True" label="Maximum possible length of the assembled sequences"
            help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" />

        <param name="min_assembly_length" type="integer" value="50" optional="True" label="Minimum possible length of the assembled sequences"
            help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" />

        <param name="min_trim_length" type="integer" value="1" optional="True" label="Minimum length of reads after trimming the low quality part"
            help="See option -q. (--min-trim-length)" />

        <param name="quality_threshold" type="integer" value="0" optional="True" label="Quality score threshold for trimming the low quality part of a read"
                help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. (--quality-threshold)" />

        <param name="max_uncalled_base" type="float" value="1.0" min="0" optional="True" max="1" label="Maximal proportion of uncalled bases in a read"
            help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases. (--max-uncalled-base)" />

        <param name="cap" type="integer" value="40" optional="True" label="Specify  the upper bound for the resulting quality score"
            help="If set to zero, capping is disabled. (--cap)" />

        <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)">
            <option value="1" selected="True">Given the minimum allowed overlap, test using the highest OES (1)</option>
            <option value="2">Use the acceptance probability (2)</option>
        </param>

        <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false"
            label="Disable empirical base frequencies" help="(--empirical-freqs)" />
        <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false"
            label="Use N base if uncertain" help="When  merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)" />

        <param name="score_method" type="select" label="Scoring method" help="(--score-method)">
            <option value="1">OES with +1 for match and -1 for mismatch</option>
            <option value="2" selected="True">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option>
            <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option>
        </param>

        <param name="outputs" type="select" display="checkboxes" optional="False" multiple="True" label="Output files">
            <option value="assembled" selected="True">Assembled reads</option>
            <option value="forward">Forward unassembled reads</option>
            <option value="reverse">Reverse unassembled reads</option>
            <option value="discarded">Discarded reads</option>
        </param>
    </inputs>
    <outputs>
        <data format="fastq" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads">
            <filter>'assembled' in outputs</filter>
        </data>
        <data format="fastq" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads">
            <filter>'forward' in outputs</filter>
        </data>
        <data format="fastq" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">
            <filter>'reverse' in outputs</filter>
        </data>
        <data format="fastq" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">
            <filter>'discarded' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="forward" value="forward.fastq" ftype="fastq" />
            <param name="reverse" value="reverse.fastq" ftype="fastq" />
            <param name="min_overlap" value="10" />
            <param name="min_assembly_length" value="50" />
            <param name="cap" value="0" />
            <param name="outputs" value="assembled,forward" />
            <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastq"/>
            <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastq"/>
        </test>
    </tests>
    <help>
<![CDATA[


**What it does**

PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger.
PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment
size as input. In addition, it implements a statistical test for minimizing false-positive results.
Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes
on a standard desktop computer.

For more information please look at the documentation_ and `github repository`_.

.. _PEAR: http://sco.h-its.org/exelixis/web/software/pear/
.. _documentation: http://sco.h-its.org/exelixis/web/software/pear/doc.html
.. _github repository: https://github.com/xflouris/PEAR


]]>
  </help>
  <citations>
      <citation type="doi">10.1093/bioinformatics/btt593</citation>
  </citations>
</tool>