comparison jbrowse2.xml @ 19:bde6b1d09f7d draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty

18:2e6c48910819

 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_2" profile="22.05">
    <description>genome browser</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edamInc"/>

        <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
<root>
    <metadata>
        <genomes>
            #if str($reference_genome.genome_type_select) == "indexed":
              <genome path="${reference_genome.genomes.fields.path}" label="${reference_genome.genomes.fields.name}">
                  <metadata />
              </genome>
            #else
              <genome path="$reference_genome.genome" label="${reference_genome.genome.element_identifier}">
                <metadata>
                  <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
                      size="${reference_genome.genome.get_size(nice_size=True)}"
                      edam_format="${reference_genome.genome.datatype.edam_format}"
                      file_ext="${reference_genome.genome.ext}"
                      dname = "${reference_genome.genome.element_identifier}" />
                  <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
                      #if $reference_genome.genome.history.user:
                      user_email="${reference_genome.genome.history.user.email}"
                      user_id="${reference_genome.genome.history.user_id}"
                      display_name="${reference_genome.genome.history.get_display_name()}"/>

                  #end if
                </gff>
            #else if str($track.data_format.data_format_select) == "synteny":
                <synteny>
                    <genome>${track.data_format.synteny_genome}</genome>
                    <genome_label>${track.data_format.synteny_genome.element_identifier}</genome_label>
                </synteny>
            #else if str($track.data_format.data_format_select) == "hic":
                <hic>
                </hic>
            #else if str($track.data_format.data_format_select) == "sparql":

            <repeat name="data_tracks" title="Annotation Track">
                <conditional name="data_format" label="Track Data Selection Options">
                    <param type="select" label="Track Type" name="data_format_select">
                        <option value="pileup">BAM Pileup track</option>
                        <option value="wiggle">BigWig track</option>
                        <!-- <option value="blast">Blast XML track - converted to GFF</option> -->
                        <option value="cram">CRAM</option>
                        <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
                        <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
                        <option value="sparql">SPARQL</option>
                        <option value="synteny">Synteny track with PAF data</option>
                       <option value="vcf">VCF SNP annotation</option>
                    </param>
                    <!--
                    <when value="blast">
                        <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                        <param label="Features used in Blast Search"
                            help="in GFF3. This is used  so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."

                            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"/>
                        <expand macro="track_visibility" />
                    </when>

                    </when>
                    <when value="cram">
                        <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="wiggle">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />

                    </when>

                    <when value="synteny">
                        <param label="Comparison genome sequence" help="Paf must use this as the reference to map the real reference sequence"
                            format="fasta"
                            name="synteny_genome"
                            type="data" />

                        <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">
                        <!-- TODO no hic datatype by default, but input for hicConvertFormat? hic_matrix datatype on .eu -->
                        <expand macro="input_conditional" label="HiC data" format="hic" />
                        <expand macro="track_visibility" />
                    </when>

                    <when value="sparql">

        <expand macro="general_options" />

        <param type="hidden" name="uglyTestingHack" value="" />
    </inputs>
    <outputs>
        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier"/>
    </outputs>
    <tests>
         <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>

19:bde6b1d09f7d

 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_3" profile="22.05">
    <description>genome browser</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edamInc"/>

        <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
<root>
    <metadata>
        <genomes>
            #if str($reference_genome.genome_type_select) == "indexed":
              <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}">
                  <metadata>
                     <dataset
                      dname = "${reference_genome.genome.name}" />
                  </metadata>
              </genome>
            #else
              <genome path="$reference_genome.genome" label="${reference_genome.genome.name}">
                <metadata>
                  <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
                      size="${reference_genome.genome.get_size(nice_size=True)}"
                      edam_format="${reference_genome.genome.datatype.edam_format}"
                      file_ext="${reference_genome.genome.ext}"
                      dname = "${reference_genome.genome.name}" />
                  <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
                      #if $reference_genome.genome.history.user:
                      user_email="${reference_genome.genome.history.user.email}"
                      user_id="${reference_genome.genome.history.user_id}"
                      display_name="${reference_genome.genome.history.get_display_name()}"/>

                  #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) == "sparql":

            <repeat name="data_tracks" title="Annotation Track">
                <conditional name="data_format" label="Track Data Selection Options">
                    <param type="select" label="Track Type" name="data_format_select">
                        <option value="pileup">BAM Pileup track</option>
                        <option value="wiggle">BigWig track</option>
                        <option value="blast">Blast XML track - converted to GFF</option>
                        <option value="cram">CRAM</option>
                        <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
                        <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
                        <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</option>
                        <option value="sparql">SPARQL</option>
                        <option value="synteny">Synteny track with PAF data</option>
                       <option value="vcf">VCF SNP annotation</option>
                    </param>
                    <when value="blast">
                        <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                        <param label="Features used in Blast Search"
                            help="in GFF3. This is used  so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."

                            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"/>
                        <expand macro="track_visibility" />
                    </when>

                    </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="wiggle">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="synteny">
                        <param label="Comparison genome sequence" help="Paf must use this as the reference to map the real reference sequence"
                            format="fasta"
                            name="synteny_genome"
                            type="data" />
                        <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="sparql">

        <expand macro="general_options" />

        <param type="hidden" name="uglyTestingHack" value="" />
    </inputs>
    <outputs>
        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name"/>
    </outputs>
    <tests>
         <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>