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comparison macros.xml @ 7:eb38b7dc3810 draft

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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
author gbcs-embl-heidelberg
date Mon, 05 Mar 2018 07:13:20 -0500
parents 7e47f78590cc
children a79f67128fc3
comparison
equal deleted inserted replaced
6:7e47f78590cc 7:eb38b7dc3810
1 <macros> 1 <macros>
2 2
3 <token name="@VERSION_STRING@">1.2</token> 3 <token name="@VERSION_STRING@">1.2.1</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.2">je-suite</requirement> 6 <requirement type="package" version="1.2">je-suite</requirement>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
276 </option> 276 </option>
277 </param> 277 </param>
278 </xml> 278 </xml>
279 279
280 <token name="@demultiplexer_common_output_options_cmd@"> 280 <token name="@demultiplexer_common_output_options_cmd@">
281 KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ 281 KEEP_UNASSIGNED_READ=${KEEP_UNASSIGNED_READ}
282 STATS_ONLY=${adv_options.STATS_ONLY} 282 STATS_ONLY=${STATS_ONLY}
283 #if str( $adv_options.DIAG ) == "true": 283 #if str( $DIAG ) == "true":
284 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE 284 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
285 #end if 285 #end if
286 </token> 286 </token>
287 <xml name="demultiplexer_common_output_options"> 287 <xml name="demultiplexer_common_output_options">
288 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" 288 <!--<section name="output_options" title="Output Options" expanded="True">-->
289 truevalue="true" 289 <param name="COLLECT_OUTPUTS" type="boolean"
290 falsevalue="false" 290 truevalue="true" falsevalue="false" checked="false"
291 checked="true" 291 label="Output forward and reverse reads in dataset collections" />
292 /> 292 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
293 <section name="adv_options" title="Advanced Options" expanded="False"> 293 truevalue="true" falsevalue="false" checked="true"/>
294 <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)"
295 truevalue="true" falsevalue="false" checked="false" 295 truevalue="true" falsevalue="false" checked="false"
296 help="This file will 296 help="This file will
297 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no 297 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no
298 match is found according to matching parameters. This file is useful for debugging or further 298 match is found according to matching parameters. This file is useful for debugging or further
299 processing in case both ends are barcoded."/> 299 processing in case both ends are barcoded."/>
300 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)" 300 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
301 truevalue="true" falsevalue="false" checked="false" 301 truevalue="true" falsevalue="false" checked="false"
302 help="do not demultiplex." /> 302 help="do not demultiplex." />
303 </section> 303 <!--</section>-->
304 </xml> 304 </xml>
305 305
306 <token name="@common_options_cmd@"> 306 <token name="@common_options_cmd@">
307 XT=${XT} 307 XT=${XT}
308 ZT=${ZT} 308 ZT=${ZT}
331 </xml> 331 </xml>
332 332
333 <token name="@demultiplexer_common_outputs_cmd@"> 333 <token name="@demultiplexer_common_outputs_cmd@">
334 METRICS_FILE_NAME=$METRICS_FILE_NAME 334 METRICS_FILE_NAME=$METRICS_FILE_NAME
335 </token> 335 </token>
336
336 <xml name="demultiplexer_common_outputs"> 337 <xml name="demultiplexer_common_outputs">
337 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result"> 338 <data name="DEMULTIPLEX_RESULTS" format="tabular" label="Je-Demultiplex result placeholder" hidden="true">
338 <!--<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="fastqsanger"--> 339 <filter>COLLECT_OUTPUTS == False and STATS_ONLY == False</filter>
339 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/> 340 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
340 </data> 341 </data>
342 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex Metrics"/>
341 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics"> 343 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
342 <filter>(adv_options['DIAG'] == 'true')</filter> 344 <filter>DIAG</filter>
343 </data> 345 </data>
346 <collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" >
347 <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
348 <discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsangar" directory="results" visible="false" />
349 </collection>
350 <collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" >
351 <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
352 <discover_datasets pattern="(?P&lt;designation&gt;.+_2\..+)" ext="fastqsangar" directory="results" visible="false" />
353 </collection>
344 </xml> 354 </xml>
345 <xml name="citations"> 355 <xml name="citations">
346 <citations> 356 <citations>
347 <citation type="doi">10.1186/s12859-016-1284-2</citation> 357 <citation type="doi">10.1186/s12859-016-1284-2</citation>
348 </citations> 358 </citations>