comparison bismark_methylation_extractor.xml @ 3:91f07ff056ca draft

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2:82814a8a2395

<tool id="bismark_methylation_extractor" name="Bismark" version="0.7.12">
    <!-- Wrapper compatible with Bismark version 0.7.7 -->
    <description>methylation extractor</description>
    <!--<version_command>bismark_methylation_extractor version</version_command>-->
    <requirements>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
        <requirement type="package" version="0.12.8">bowtie</requirement>
        <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
    </requirements>
    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_methylation_extractor.py

        #end if

    </command>
    <inputs>
        <!-- Input Parameters -->
        <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" />
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library mate-paired?">
              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single" />
            <when value="paired">
                <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" />
            </when>
        </conditional>

       <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" />
       <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info
into context-dependent output files" help="" />
       <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." />
       <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" />

3:91f07ff056ca

<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.1">
    <!-- Wrapper compatible with Bismark version 0.10 -->
    <description>Reports on methylation status of reads mapped by Bismark</description>
    <!--<version_command>bismark_methylation_extractor version</version_command>-->
    <requirements>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
        <requirement type="package" version="0.12.8">bowtie</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
    </requirements>
    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_methylation_extractor.py

        #end if

    </command>
    <inputs>
        <!-- Input Parameters -->
        <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" />
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library mate-paired?">
              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single" />
            <when value="paired">
                <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" />
            </when>
        </conditional>
       <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" />
       <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info
into context-dependent output files" help="" />
       <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." />
       <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" />