comparison jbrowse2.xml @ 57:94264fe60478 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty

56:c0097a584a8a

                              </trackFile>
                       #end for
                    </files>

                    <options>

                    #if str($track.data_format.data_format_select) == "bam":
                        <bam>
                            #for $dataset in $track.data_format.useuri.annotation:
                                <bam_index>${dataset.metadata.bam_index}</bam_index>
                            #end for

                        <param label="Is this a protein blast search?"
                            type="boolean"
                            name="is_protein"
                            truevalue="true"
                            falsevalue="false" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="vcf">
                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
                        <expand macro="track_styling_vcf"/>

                                    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" />
                    </when>
                    <when value="bam">
                        <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bed">
                        <expand macro="input_conditional" label="BED Track Data" format="bed" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="cram">
                        <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="maf">
                        <expand macro="input_conditional" label="MAF Track Data" format="maf" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bigwig">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />

57:94264fe60478

                              </trackFile>
                       #end for
                    </files>

                    <options>
                        <style>
                        #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "paf", "maf", "blastxml"]:
                            <type>${track.data_format.jbstyle.track_style.display}</type>
                            #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
                                <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
                                <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
                            #end if
                        #end if
                        #if str($track.data_format.data_format_select) in ["bam", "cram"]:
                            <type>"LinearAlignmentsDisplay"</type>
                        #end if
                        </style>
                    #if str($track.data_format.data_format_select) == "bam":
                        <bam>
                            #for $dataset in $track.data_format.useuri.annotation:
                                <bam_index>${dataset.metadata.bam_index}</bam_index>
                            #end for

                        <param label="Is this a protein blast search?"
                            type="boolean"
                            name="is_protein"
                            truevalue="true"
                            falsevalue="false" />
                        <expand macro="track_styling_feature" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="vcf">
                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
                        <expand macro="track_styling_vcf"/>

                                    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_styling_feature" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bam">
                        <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bed">
                        <expand macro="input_conditional" label="BED Track Data" format="bed" />
                        <expand macro="track_styling_feature" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="cram">
                        <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="maf">
                        <expand macro="input_conditional" label="MAF Track Data" format="maf" />
                        <expand macro="track_styling_feature" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bigwig">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />