comparison teloscope.xml @ 2:321ceb58023e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 201733bc2332c99e30f65ae90a3c2f299153fff2

1:6c1cfce7c2eb

            $out_entropy
            $out_matches
            $out_its
            $ultra_fast
            $verbose
            > output/${input_sequence.name}.telo.report
    ]]></command>
    <inputs>
        <param argument="--input-sequence" type="data" format="fasta,fasta.gz" label="Input assembly"/>
        <param argument="--canonical" type="text" value="TTAGGG" label="Canonical telomeric pattern">
            <sanitizer>

    </inputs>

    <outputs>
        <!-- BASIC OUTFILES -->
        <data name="terminal_telomeres" format="bed" from_work_dir="output/*_terminal_telomeres.bed" label="${tool.name} on ${on_string}: Terminal telomeres"/>
        <data name="telo_report" format="tabular" from_work_dir="output/*.telo.report" label="${tool.name} on ${on_string}: Summary report"/>

        <!-- OPTIONAL OUTFILES -->
        <data name="interstitial_telomeres" format="bed" from_work_dir="output/*_interstitial_telomeres.bed" label="${tool.name} on ${on_string}: Interstitial telomeres">
            <filter>out_its</filter>
        </data>

                </assert_contents>
            </output>
            <output name="telo_report">
                <assert_contents>
                    <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
                </assert_contents>
            </output>
        </test>

        <!-- 4) Edit distance 2: maximum variants detected -->

                </assert_contents>
            </output>
            <output name="telo_report">
                <assert_contents>
                    <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    

2:321ceb58023e

            $out_entropy
            $out_matches
            $out_its
            $ultra_fast
            $verbose
            > '$telo_report'
    ]]></command>
    <inputs>
        <param argument="--input-sequence" type="data" format="fasta,fasta.gz" label="Input assembly"/>
        <param argument="--canonical" type="text" value="TTAGGG" label="Canonical telomeric pattern">
            <sanitizer>

    </inputs>

    <outputs>
        <!-- BASIC OUTFILES -->
        <data name="terminal_telomeres" format="bed" from_work_dir="output/*_terminal_telomeres.bed" label="${tool.name} on ${on_string}: Terminal telomeres"/>
        <data name="telo_report" format="tabular" label="${tool.name} on ${on_string}: Summary report"/>

        <!-- OPTIONAL OUTFILES -->
        <data name="interstitial_telomeres" format="bed" from_work_dir="output/*_interstitial_telomeres.bed" label="${tool.name} on ${on_string}: Interstitial telomeres">
            <filter>out_its</filter>
        </data>

                </assert_contents>
            </output>
            <output name="telo_report">
                <assert_contents>
                    <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
                    <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/>
                    <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/>
                    <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/>
                    <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/>
                </assert_contents>
            </output>
        </test>

        <!-- 4) Edit distance 2: maximum variants detected -->

                </assert_contents>
            </output>
            <output name="telo_report">
                <assert_contents>
                    <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
                    <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/>
                    <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/>
                    <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/>
                    <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/>
                </assert_contents>
            </output>
        </test>
    </tests>