Mercurial > repos > fubar > jbrowse2

comparison macros.xml @ 46:4181e97c70a7 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
author fubar
date Mon, 04 Mar 2024 09:47:19 +0000
parents 0ec526d2d8c1
children 460d5b6c5d98
comparison
equal deleted inserted replaced
45:0ec526d2d8c1 46:4181e97c70a7
138 </param> 138 </param>
139 </xml> 139 </xml>
140 140
141 <xml name="general_options"> 141 <xml name="general_options">
142 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> 142 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
143 <conditional name="ucol">
144 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form"
145 help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically">
146 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option>
147 <option value="collect">Convert a collection of suitable track files</option>
148 </param>
149 <when value="collect">
150 <param label="Collection of bed, bam and other track files" name="autoCollection" type="data_collection" />
151 </when>
152 <when value="form">
153 </when>
154 </conditional>
155
143 <param label="Create a zip archive for downloading rather than viewing " name="zipOut" help="Default is to make an interactive browser appear when the 'eye' icon is activated" 156 <param label="Create a zip archive for downloading rather than viewing " name="zipOut" help="Default is to make an interactive browser appear when the 'eye' icon is activated"
144 type="boolean" checked="false" truevalue="true" falsevalue="false" /> 157 type="boolean" checked="false" truevalue="true" falsevalue="false" />
145 <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/> 158 <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/>
146 <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/> 159 <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/>
147 <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" /> 160 <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" />
503 </valid> 516 </valid>
504 </sanitizer> 517 </sanitizer>
505 </xml> 518 </xml>
506 519
507 <xml name="input_conditional" token_label="Track Data" token_format="data"> 520 <xml name="input_conditional" token_label="Track Data" token_format="data">
508 <param label="@LABEL@" format="@FORMAT@" name="annotation" optional="True" type="data" multiple="True"/> 521 <conditional name="useuri">
509 </xml> 522 <param name="insource" type="select" label="Define track data as a history file or an internet URI"
523 help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
524 <option value="history" selected="true">Track data from a history file</option>
525 <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option>
526 </param>
527 <when value="history">
528 <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
529 </when>
530 <when value="uri">
531 <param label="@LABEL@" name="annouri" multiple="false" type="text" />
532 <param label="Short name for track display" name="annoname" type="text" >
533 <sanitizer invalid_char="_">
534 <valid initial="string.printable" >
535 <remove value="'" />
536 </valid>
537 </sanitizer>
538 </param>
539 </when>
540 </conditional>
541 </xml>
510 <xml name="citations"> 542 <xml name="citations">
511 <citations> 543 <citations>
512 <citation type="doi">10.1186/s13059-016-0924-1</citation> 544 <citation type="doi">10.1186/s13059-016-0924-1</citation>
513 <citation type="doi">10.1101/gr.094607.109</citation> 545 <citation type="doi">10.1101/gr.094607.109</citation>
514 </citations> 546 </citations>