comparison split_libraries.xml @ 7:481efc8a2fe2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 358f82bc5a70186b8fc917fe0f5323a330051b8e

6:2a39329e51c5

    </inputs>
    <outputs>
        <data name="sequences" format="fasta" from_work_dir="split_libraries/*.fna" label="${tool.name} on ${on_string}: sequences"/>
        <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
        <data name="histograms" format="txt" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
        <data name="quality" format="qual,qual454,qualillumina,qualsolexa,qualsolid" from_work_dir="split_libraries/*.qual" label="${tool.name} on ${on_string}: quality">
            <filter>add_qual['record_qual_scores']!=""</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="map" value="split_libraries/mapping_file.txt"/>
            <param name="fasta" value="split_libraries/reads_1.fna,split_libraries/reads_2.fna"/>
            <param name="add_qual_test" value="true"/>
            <param name="qual" value="split_libraries/reads_1.qual,split_libraries/reads_2.qual"/>
            <param name="min_qual_score" value="25"/>
            <param name="qual_score_window" value="0"/>
            <param name="discard_bad_windows" value=""/>
            <param name="record_qual_scores" value="--record_qual_scores"/>
            <param name="min_seq_length" value="200" />

                    <has_text text="bc_diffs" />
                </assert_contents>
            </output>
            <output name="log" file="split_libraries/split_library_log"/>
            <output name="histograms" file="split_libraries/histograms.txt"/>
            <output name="quality">
                <assert_contents>
                    <has_text text="PC.634_1" />
                    <has_text text="bc_diffs" />
                </assert_contents>
            </output>

7:481efc8a2fe2

    </inputs>
    <outputs>
        <data name="sequences" format="fasta" from_work_dir="split_libraries/*.fna" label="${tool.name} on ${on_string}: sequences"/>
        <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
        <data name="histograms" format="txt" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
        <data name="quality" format_source="qual" from_work_dir="split_libraries/*.qual" label="${tool.name} on ${on_string}: quality">
            <filter>'record_qual_scores' in add_qual and add_qual['record_qual_scores']</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="map" value="split_libraries/mapping_file.txt"/>
            <param name="fasta" value="split_libraries/reads_1.fna,split_libraries/reads_2.fna"/>
            <param name="add_qual_test" value="true"/>
            <param name="qual" ftype="qualillumina" value="split_libraries/reads_1.qual,split_libraries/reads_2.qual"/>
            <param name="min_qual_score" value="25"/>
            <param name="qual_score_window" value="0"/>
            <param name="discard_bad_windows" value=""/>
            <param name="record_qual_scores" value="--record_qual_scores"/>
            <param name="min_seq_length" value="200" />

                    <has_text text="bc_diffs" />
                </assert_contents>
            </output>
            <output name="log" file="split_libraries/split_library_log"/>
            <output name="histograms" file="split_libraries/histograms.txt"/>
            <output name="quality" ftype="qualillumina">
                <assert_contents>
                    <has_text text="PC.634_1" />
                    <has_text text="bc_diffs" />
                </assert_contents>
            </output>