comparison bismark_methylation_extractor.xml @ 22:8c191acde702 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35

21:120b7b35e442

<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1" profile="18.01">
    <description>Reports on methylation status of reads mapped by Bismark</description>
    <requirements>
        <requirement type="package" version="0.22.1">bismark</requirement>
        <requirement type="package" version="1.8">samtools</requirement>
        <requirement type="package" version="2.3.5">bowtie2</requirement>
    </requirements>
    <command><![CDATA[
        python '$__tool_directory__/bismark_methylation_extractor.py'

        --multicore "\${GALAXY_SLOTS:-4}"

          --mbias_report '$output_mbias_report'
        #end if

        #if $cytosine_report['cytosine_report_selector']:
          --cytosine_report '$output_cytosine_report'
          #if $cytosine_report.refGenomeSource.genomeSource == "built_in_fasta":
            --genome_file '${cytosine_report.refGenomeSource.built_in_fasta.fields.path}'
          #else:
            --genome_file '$cytosine_report.refGenomeSource["own_file"]'
          #end if

                        <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
                    </when>
                </conditional>
                <param name="cpg_context" type="boolean" truevalue="true" falsevalue="false" checked="False"
                       label="Reports Cpg Context only"/>
            </when>
            <when value="false"></when>
        </conditional>
        <section name="output_settings" title="Advanced output settings" expanded="False">
            <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="True"

        </data>
        <data format="txt" name="output_cytosine_report"
              label="${tool.name} on ${on_string}: Genome-wide methylation report.">
            <filter>( cytosine_report['cytosine_report_selector'] )</filter>
        </data>
        <data format="zip" name="compressed_output" label="${tool.name} on ${on_string}: Result archive."/>
        <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
            <filter>( output_settings['separate_logfile'] is True )</filter>
        </data>
    </outputs>

                    <has_line line="chrY_JH584303_random&#009;4&#009;+&#009;0&#009;0&#009;CHH&#009;CAT" />
                    <has_line line="chrY_JH584301_random&#009;259872&#009;-&#009;0&#009;0&#009;CHH&#009;CAT" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>
        <![CDATA[

22:8c191acde702

<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1+galaxy1" profile="18.01">
    <description>Reports on methylation status of reads mapped by Bismark</description>
    <requirements>
        <requirement type="package" version="0.22.1">bismark</requirement>
        <requirement type="package" version="1.8">samtools</requirement>
        <requirement type="package" version="2.4.4">bowtie2</requirement>
    </requirements>
    <command><![CDATA[
        python '$__tool_directory__/bismark_methylation_extractor.py'

        --multicore "\${GALAXY_SLOTS:-4}"

          --mbias_report '$output_mbias_report'
        #end if

        #if $cytosine_report['cytosine_report_selector']:
          --cytosine_report '$output_cytosine_report'
          #if  $cytosine_report['coverage_output']:
            --coverage_file '$coverage_file'
          #end if
          #if $cytosine_report.refGenomeSource.genomeSource == "built_in_fasta":
            --genome_file '${cytosine_report.refGenomeSource.built_in_fasta.fields.path}'
          #else:
            --genome_file '$cytosine_report.refGenomeSource["own_file"]'
          #end if

                        <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
                    </when>
                </conditional>
                <param name="cpg_context" type="boolean" truevalue="true" falsevalue="false" checked="False"
                       label="Reports Cpg Context only"/>
                <param name="coverage_output" type="boolean" truevalue="true" falsevalue="false" checked="False"
                       label="Generate Bismark coverage report"/>
                
            </when>
            <when value="false"></when>
        </conditional>
        <section name="output_settings" title="Advanced output settings" expanded="False">
            <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="True"

        </data>
        <data format="txt" name="output_cytosine_report"
              label="${tool.name} on ${on_string}: Genome-wide methylation report.">
            <filter>( cytosine_report['cytosine_report_selector'] )</filter>
        </data>
        <data format="tabular.gz" name="coverage_file"
              label="${tool.name} on ${on_string}:Coverage file.">
            <filter>( cytosine_report['cytosine_report_selector'] and cytosine_report['coverage_output'])</filter>
        </data>
        <data format="zip" name="compressed_output" label="${tool.name} on ${on_string}: Result archive."/>
        <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
            <filter>( output_settings['separate_logfile'] is True )</filter>
        </data>
    </outputs>

                    <has_line line="chrY_JH584303_random&#009;4&#009;+&#009;0&#009;0&#009;CHH&#009;CAT" />
                    <has_line line="chrY_JH584301_random&#009;259872&#009;-&#009;0&#009;0&#009;CHH&#009;CAT" />
                </assert_contents>
            </output>
        </test>
        <!--Test coverage output -->
        <test>
            <param name="input" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
            <param name="sPaired" value="single"/>
            <param name="cytosine_report_selector" value="true"/>
            <param name="genomeSource" value="history"/>
            <param name="own_file" value="mm10.tiny.fa.gz" />
            <param name="coverage_output" value="true"/>
            <output name="coverage_file" ftype="tabular.gz">
                <assert_contents>
                    <has_size value="19960" delta="300"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>
        <![CDATA[