comparison macros.xml @ 60:81d535970196 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a

59:f807e219cec3

            </conditional>
     </xml>
    <xml name="pafref_conditional" token_label="Track Data" token_format="data">
        <conditional name="pafuseuri">
                <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?"
                    help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
                    <option value="history" selected="true">PAF genome reference data from a history file</option>
                    <option value="uri">PAF genome reference data from tabix data URI - index files must be available at corresponding URI</option>
                </param>
                <when value="history">
                    <repeat name="refgenomes" title="Add one or more comparison genomes used to make the PAF">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                       <param label="Short name for track display" name="annoname" type="text" >
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />

                              </sanitizer>
                        </param>
                    </repeat>
                </when>
                <when value="uri">
                    <repeat name="refgenomes" title="Provide URI for a comparison genomesused to make the PAF">
                       <param label="@LABEL@" name="annotation"  type="text" />
                       <param label="Short name for track display" name="annoname" type="text" >
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />

60:81d535970196

            </conditional>
     </xml>
    <xml name="pafref_conditional" token_label="Track Data" token_format="data">
        <conditional name="pafuseuri">
                <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?"
                    help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
                    <option value="history" selected="true">PAF reference comparison genome from a history file</option>
                    <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
                </param>
                <when value="history">
                    <repeat name="refgenomes" title="PAF reference comparison genome used to make the PAF">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                       <param label="Short name for track display" name="annoname" type="text" >
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />

                              </sanitizer>
                        </param>
                    </repeat>
                </when>
                <when value="uri">
                    <repeat name="refgenomes" title="PAF reference comparison genome URI">
                       <param label="@LABEL@" name="annotation"  type="text" />
                       <param label="Short name for track display" name="annoname" type="text" >
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />