comparison jbrowse2.xml @ 27:4ff1ed2065cc draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty

26:e578621acb13

                <gff>
                  #if $track.data_format.match_part.match_part_select == "true":
                    <match>${track.data_format.match_part.name}</match>
                  #end if
                </gff>
            #else if str($track.data_format.data_format_select) == "synteny":
                <synteny>
                    <genome>${track.data_format.synteny_genome}</genome>
                    <genome_label>${track.data_format.synteny_genome.name}</genome_label>
                </synteny>
            #else if str($track.data_format.data_format_select) == "hic":
                <hic>
                </hic>
            #else if str($track.data_format.data_format_select) == "cool":
                <cool>

                            <when value="true">
                                <param label="Match Part Feature Type"
                                    name="name"
                                    type="text"
                                    value="match"
                                    help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
                                    optional="True"/>
                            </when>
                            <when value="false" />
                        </conditional>
                        <expand macro="track_visibility" />

                        <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/>
                        <expand macro="track_visibility" />
                    </when>

                    <when value="hic">
                        <expand macro="input_conditional" label="HiC data" format="hic" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="cool">
                        <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" />
                        <expand macro="track_visibility" />

27:4ff1ed2065cc

                <gff>
                  #if $track.data_format.match_part.match_part_select == "true":
                    <match>${track.data_format.match_part.name}</match>
                  #end if
                </gff>
            #else if str($track.data_format.data_format_select) == "paf":
                <paf>
                    <genome>${track.data_format.synteny_genome}</genome>
                    <genome_label>${track.data_format.synteny_genome.name}</genome_label>
                </paf>
            #else if str($track.data_format.data_format_select) == "hic":
                <hic>
                </hic>
            #else if str($track.data_format.data_format_select) == "cool":
                <cool>

                            <when value="true">
                                <param label="Match Part Feature Type"
                                    name="name"
                                    type="text"
                                    value="match"
                                    help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
                                    optional="True"/>
                            </when>
                            <when value="false" />
                        </conditional>
                        <expand macro="track_visibility" />

                        <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/>
                        <expand macro="track_visibility" />
                    </when>

                    <when value="hic">
                        <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="cool">
                        <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" />
                        <expand macro="track_visibility" />