comparison macros.xml @ 59:f807e219cec3 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9

58:0e592dcaeb7f

    <xml name="input_conditional" token_label="Track Data" token_format="data">
        <conditional name="useuri">
                <param name="insource" type="select" label="Define track data as 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">Track data from a history file</option>
                    <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option>
                </param>
                <when value="history">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                </when>
                <when value="uri">

                              </sanitizer>
                        </param>
                </when>
            </conditional>
     </xml>
    <xml name="citations">
        <citations>
        <citation type="doi">10.1186/s13059-016-0924-1</citation>
        <citation type="doi">10.1101/gr.094607.109</citation>
        </citations>

59:f807e219cec3

    <xml name="input_conditional" token_label="Track Data" token_format="data">
        <conditional name="useuri">
                <param name="insource" type="select" label="Define track data as 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">Track data from a history file</option>
                    <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option>
                </param>
                <when value="history">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                </when>
                <when value="uri">

                              </sanitizer>
                        </param>
                </when>
            </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="'" />
                                </valid>
                              </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="'" />
                                </valid>
                              </sanitizer>
                        </param>
                    </repeat>
                </when>
            </conditional>
     </xml>
    <xml name="citations">
        <citations>
        <citation type="doi">10.1186/s13059-016-0924-1</citation>
        <citation type="doi">10.1101/gr.094607.109</citation>
        </citations>