Mercurial > repos > gbcs-embl-heidelberg > je_clip

comparison macros.xml @ 5:8b4ccdf5f7dd draft

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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
author gbcs-embl-heidelberg
date Wed, 02 Aug 2017 10:58:49 -0400
parents 9d85f5915da9
children 3c7fa5621091
comparison
equal deleted inserted replaced
4:9d85f5915da9 5:8b4ccdf5f7dd
1 <macros> 1 <macros>
2 2
3 <token name="@VERSION_STRING@">1.2</token> 3 <token name="@VERSION_STRING@">1.2</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="1.2">je-suite</requirement>
7 </requirements>
8 </xml>
9 <xml name="version_command">
10 <version_command>je version 2&gt;&amp;1 | tail -n 1</version_command>
11 </xml>
4 12
5 <token name="@single_or_paired_cmd@"> 13 <token name="@single_or_paired_cmd@">
6 #if str( $library.type ) == "single": 14 #if str( $library.type ) == "single":
7 F1=${library.input_1} 15 F1=${library.input_1}
8 #elif str( $library.type ) == "paired": 16 #elif str( $library.type ) == "paired":
276 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE 284 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
277 #end if 285 #end if
278 </token> 286 </token>
279 <xml name="demultiplexer_common_output_options"> 287 <xml name="demultiplexer_common_output_options">
280 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" 288 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
281 truealue="true" 289 truevalue="true"
282 falsevalue="false" 290 falsevalue="false"
283 checked="true" 291 checked="true"
284 /> 292 />
285 <section name="adv_options" title="Advanced Options" expanded="False"> 293 <section name="adv_options" title="Advanced Options" expanded="False">
286 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)" 294 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
315 <param name="RCHAR" type="text" 323 <param name="RCHAR" type="text"
316 label="Replace white space in the read name/header with speficied symbols (RCHAR)" 324 label="Replace white space in the read name/header with speficied symbols (RCHAR)"
317 help="Set to empty or null for no replacement." 325 help="Set to empty or null for no replacement."
318 value=":"/> 326 value=":"/>
319 327
320 <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)" 328 <param name="GZ" type="hidden" label="Compress output (GZ)"
321 help="will result in fastq.gz files." 329 help="will result in fastq.gz files."
322 truevalue="true" 330 value="false"/>
323 falsevalue="false"
324 checked="false"/>
325 </xml> 331 </xml>
326 332
327 <token name="@demultiplexer_common_outputs_cmd@"> 333 <token name="@demultiplexer_common_outputs_cmd@">
328 METRICS_FILE_NAME=$METRICS_FILE_NAME 334 METRICS_FILE_NAME=$METRICS_FILE_NAME
329 </token> 335 </token>
334 </data> 340 </data>
335 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics"> 341 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
336 <filter>(adv_options['DIAG'] == 'true')</filter> 342 <filter>(adv_options['DIAG'] == 'true')</filter>
337 </data> 343 </data>
338 </xml> 344 </xml>
339 345 <xml name="citations">
346 <citations>
347 <citation type="doi">10.1186/s12859-016-1284-2</citation>
348 </citations>
349 </xml>
340 </macros> 350 </macros>