comparison jbrowse2.xml @ 38:07849bf248e3 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767

37:7adde511daa1

    <command detect_errors="aggressive"><![CDATA[
mkdir -p '$output.files_path' &&
## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp '$trackxml' '$output.files_path/galaxy.xml' &&
python '$__tool_directory__/jbrowse2.py'
--outdir '$output.files_path'
--xml '$trackxml' &&
#if $jbgen.zipOut == "true":
    (cd '$output.files_path' && zip -r - . ) > '$output'
#else

            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="wiggle"/>
                        <param name="annotation" value="bw/merlin.bw"/>
                    </conditional>
                </repeat>
            </repeat>
            <param name="uglyTestingHack" value="enabled" />

                    <has_text text="history id="></has_text>
                    <has_text text="metadata"></has_text>
                    <has_text text="tool_id"></has_text>
                    <has_text text="trackFile path="></has_text>
                    <has_text text="file_ext=&quot;bigwig&quot;"></has_text>
                    <has_text text="format=&quot;wiggle&quot;"></has_text>
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />

                    <has_text text="With menu or index"/>
                    <has_text text="gene_calls"/>
                </assert_contents>
            </output>
        </test>

        <!-- TODO add a synteny test -->
        <!-- TODO add a bam and a cram test -->
        <!-- TODO add an hic test -->
        <!-- TODO add a vcf_bgzip test -->
    </tests>

38:07849bf248e3

    <command detect_errors="aggressive"><![CDATA[
mkdir -p '$output.files_path' &&
## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp '$trackxml' '$output.files_path/galaxy.xml' &&

export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&

## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse2.py'
--jbrowse2path \${JBROWSE2_PATH}
--outdir '$output.files_path'
--xml '$trackxml' &&
#if $jbgen.zipOut == "true":
    (cd '$output.files_path' && zip -r - . ) > '$output'
#else

            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="bigwig"/>
                        <param name="annotation" value="bw/merlin.bw"/>
                    </conditional>
                </repeat>
            </repeat>
            <param name="uglyTestingHack" value="enabled" />

                    <has_text text="history id="></has_text>
                    <has_text text="metadata"></has_text>
                    <has_text text="tool_id"></has_text>
                    <has_text text="trackFile path="></has_text>
                    <has_text text="file_ext=&quot;bigwig&quot;"></has_text>
                    <has_text text="format=&quot;bigwig&quot;"></has_text>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />

                    <has_text text="With menu or index"/>
                    <has_text text="gene_calls"/>
                </assert_contents>
            </output>
        </test>
        <!-- TODO add a synteny test -->
        <!-- TODO add a bam and a cram test -->
        <!-- TODO add an hic test -->
        <!-- TODO add a vcf_bgzip test -->
    </tests>