comparison salmon.xml @ 11:c320b539ff54 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72

10:d9bfffca4548

                <option value="O">Mates are oriented away from each other (O = outward)</option>
                <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
            </param>
        </xml>
        <token name="@VERSION@">0.11.2</token>
    </macros>

    <requirements>
        <requirement type="package" version="1.0.6">bzip2</requirement>
        <requirement type="package" version="@VERSION@">salmon</requirement>

                <option value="indexed">Use a built-in index</option>
                <option value="history" selected="True">Use one from the history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
                    <options from_data_table="salmon_indexes">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                    </options>
                </param>
            </when>  <!-- build-in -->
            <when value="history">

                    <has_text text="NR_031764" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test>
        <test> <!-- gzipped input -->
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
            <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
            <param name="biasCorrect" value="False" />

11:c320b539ff54

                <option value="O">Mates are oriented away from each other (O = outward)</option>
                <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
            </param>
        </xml>
        <token name="@VERSION@">0.11.2</token>
        <token name="@IDX_VERSION@">q5</token>
    </macros>

    <requirements>
        <requirement type="package" version="1.0.6">bzip2</requirement>
        <requirement type="package" version="@VERSION@">salmon</requirement>

                <option value="indexed">Use a built-in index</option>
                <option value="history" selected="True">Use one from the history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
                    <options from_data_table="salmon_indexes_versioned">
                        <filter type="sort_by" column="2"/>
                        <filter type="static_value" column="4" value="@IDX_VERSION@" />
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                    </options>
                </param>
            </when>  <!-- build-in -->
            <when value="history">

                    <has_text text="NR_031764" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test>
        <test> <!--test use of built-in index-->
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="reads_1.fastq" />
            <param name="input_mate2" value="reads_2.fastq" />
            <param name="biasCorrect" value="False" />
            <param name="TranscriptSource" value="indexed" />
            <param name="index" value="hg19_transcript_subset" />
            <output name="output_quant">
                <assert_contents>
                    <has_text text="EffectiveLength" />
                    <has_text text="TPM" />
                    <has_text text="NM_001168316" />
                    <has_text text="NM_174914" />
                    <has_text text="NM_018953" />
                    <has_text text="NR_003084" />
                    <has_text text="NM_017410" />
                    <has_text text="NM_153693" />
                    <has_text text="NR_031764" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test>
        <test> <!-- gzipped input -->
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
            <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
            <param name="biasCorrect" value="False" />