comparison bbduk.xml @ 7:4f4e34a75de9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab

6:c456a40153af

        gchist='${output_gchist}'
    #end if
    #if str($output_hists_cond.output_hists_select).find('enthist') >= 0:
        enthist='${output_enthist}'
    #end if
#end if
t=\${GALAXY_SLOTS:-4}
]]></command>
    <inputs>
        <expand macro="input_type_cond"/>

                    <option value="gchist">Read GC content histogram</option>
                    <option value="enthist">Read entropy histogram</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
            <filter>str(outputs_select).find('outu') &gt;= 0</filter>
            <filter>'outu' in outputs_select</filter>

            <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
        </data>
        <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
            <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
        </data>
    </outputs>
    <tests>
        <!-- Single read -->
        <test expect_num_outputs="1">
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
            <param name="reference_type" value="files"/>
            <param name="outputs_select" value="outu"/>
            <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
        </test>
        <!-- Paired reads in separate datasets -->
        <test expect_num_outputs="4">
            <param name="input_type" value="pair"/>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>

7:4f4e34a75de9

        gchist='${output_gchist}'
    #end if
    #if str($output_hists_cond.output_hists_select).find('enthist') >= 0:
        enthist='${output_enthist}'
    #end if
#end if
#if $log_file
    2> >(tee '$log_output' >&2)
#end if
t=\${GALAXY_SLOTS:-4}
]]></command>
    <inputs>
        <expand macro="input_type_cond"/>

                    <option value="gchist">Read GC content histogram</option>
                    <option value="enthist">Read entropy histogram</option>
                </param>
            </when>
        </conditional>
        <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/>
    </inputs>
    <outputs>
        <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
            <filter>str(outputs_select).find('outu') &gt;= 0</filter>
            <filter>'outu' in outputs_select</filter>

            <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
        </data>
        <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
            <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
        </data>
        <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)">
            <filter>log_file</filter>
        </data>
    </outputs>
    <tests>
        <!-- Single read -->
        <test expect_num_outputs="2">
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
            <param name="reference_type" value="files"/>
            <param name="outputs_select" value="outu"/>
            <param name="log_file" value="true"/>
            <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
            <output name="log_output" ftype="txt">
                <assert_contents>
                    <has_text text="Executing jgi.BBDuk"/>
                    <has_text text="Input"/>
                    <has_text text="Contaminants"/>
                    <has_text text="Total Removed"/>
                    <has_text text="Result"/>
                    <has_text text="10000 bases"/>
                    <has_text text="100 reads"/>
                    <has_text text="0 reads"/>
                    <has_text text="0 bases"/>
                </assert_contents>
            </output>
        </test>
        <!-- Paired reads in separate datasets -->
        <test expect_num_outputs="4">
            <param name="input_type" value="pair"/>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>