Mercurial > repos > gbcs-embl-heidelberg > je_markdupes

comparison macros.xml @ 2:f6bc74863c1c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
author gbcs-embl-heidelberg
date Wed, 07 Dec 2016 11:57:09 -0500
parents d39a96961423
children 4ccf1406832d
comparison
equal deleted inserted replaced
1:c6afeeade4f2 2:f6bc74863c1c
15 #end if 15 #end if
16 </token> 16 </token>
17 17
18 <xml name="paired_options"> 18 <xml name="paired_options">
19 <when value="paired"> 19 <when value="paired">
20 <param name="input_1" format="fastq" type="data" label="FASTQ file #1"/> 20 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/>
21 <param name="input_2" format="fastq" type="data" label="FASTQ file #2"/> 21 <param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/>
22 <yield /> 22 <yield />
23 <param name="SAME_HEADERS" type="boolean" 23 <param name="SAME_HEADERS" type="boolean"
24 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" 24 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
25 help="Only applies if barcodes are added to the header (option ADD)" 25 help="Only applies if barcodes are added to the header (option ADD)"
26 truevalue="true" 26 truevalue="true"
27 falsevalue="false" checked="false"/> 27 falsevalue="false" checked="false"/>
28 </when> 28 </when>
29 <when value="paired_collection"> 29 <when value="paired_collection">
30 <param name="input_1" format="fastq" type="data_collection" collection_type="paired" 30 <param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired"
31 label="FASTQ Paired Dataset"/> 31 label="FASTQ Paired Dataset"/>
32 <yield /> 32 <yield />
33 <param name="SAME_HEADERS" type="boolean" 33 <param name="SAME_HEADERS" type="boolean"
34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" 34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
35 help="Only applies if barcodes are added to the header (option ADD)" 35 help="Only applies if barcodes are added to the header (option ADD)"
58 <option value="single">Single-end</option> 58 <option value="single">Single-end</option>
59 <option value="paired">Paired-end</option> 59 <option value="paired">Paired-end</option>
60 <option value="paired_collection">Paired-end Dataset Collection</option> 60 <option value="paired_collection">Paired-end Dataset Collection</option>
61 </param> 61 </param>
62 <when value="single"> 62 <when value="single">
63 <param name="input_1" format="fastq" type="data" label="FASTQ file"/> 63 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/>
64 <param name="I1" type="data" format="fastq" label="First Index File"/> 64 <param name="I1" type="data" format="fastq,gz" label="First Index File"/>
65 </when> 65 </when>
66 <expand macro="paired_options"> 66 <expand macro="paired_options">
67 <param name="I1" type="data" format="fastq" label="First Index File"/> 67 <param name="I1" type="data" format="fastq,gz" label="First Index File"/>
68 <conditional name="I2_CONDITIONAL"> 68 <conditional name="I2_CONDITIONAL">
69 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> 69 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
70 <option value="true">Yes</option> 70 <option value="true">Yes</option>
71 <option value="false" selected="true">No</option> 71 <option value="false" selected="true">No</option>
72 </param> 72 </param>
73 <when value="true"> 73 <when value="true">
74 <param name="I2" type="data" format="fastq" label="Second Index File"/> 74 <param name="I2" type="data" format="fastq,gz" label="Second Index File"/>
75 <expand macro="bred_conditional"/> 75 <expand macro="bred_conditional"/>
76 </when> 76 </when>
77 <when value="false"/> 77 <when value="false"/>
78 </conditional> 78 </conditional>
79 </expand> 79 </expand>
86 <option value="single">Single-end</option> 86 <option value="single">Single-end</option>
87 <option value="paired">Paired-end</option> 87 <option value="paired">Paired-end</option>
88 <option value="paired_collection">Paired-end Dataset Collection</option> 88 <option value="paired_collection">Paired-end Dataset Collection</option>
89 </param> 89 </param>
90 <when value="single"> 90 <when value="single">
91 <param name="input_1" format="fastq" type="data" label="FASTQ file"/> 91 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/>
92 </when> 92 </when>
93 <expand macro="paired_options"> 93 <expand macro="paired_options">
94 <yield /> 94 <yield />
95 </expand> 95 </expand>
96 </conditional> 96 </conditional>
296 <token name="@common_options_cmd@"> 296 <token name="@common_options_cmd@">
297 XT=${XT} 297 XT=${XT}
298 ZT=${ZT} 298 ZT=${ZT}
299 #if str( $RCHAR ) != "": 299 #if str( $RCHAR ) != "":
300 RCHAR=${RCHAR} 300 RCHAR=${RCHAR}
301 #else:
302 RCHAR=null
301 #end if 303 #end if
302 GZ=${GZ} 304 GZ=${GZ}
303 OUTPUT_DIR=results 305 OUTPUT_DIR=results
304 </token> 306 </token>
305 <xml name="common_options"> 307 <xml name="common_options">
308 <param name="ZT" type="text" value="0" 310 <param name="ZT" type="text" value="0"
309 label="Extra number of bases to be trimmed from the read end (ZT)" /> 311 label="Extra number of bases to be trimmed from the read end (ZT)" />
310 312
311 <param name="RCHAR" type="text" 313 <param name="RCHAR" type="text"
312 label="Replace white space in the read name/header with speficied symbols (RCHAR)" 314 label="Replace white space in the read name/header with speficied symbols (RCHAR)"
313 help="Set to empty for no replacement" 315 help="Set to empty or null for no replacement."
314 value=":"/> 316 value=":"/>
315 317
316 <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)" 318 <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
317 help="will result in fastq.gz files." 319 help="will result in fastq.gz files."
318 truevalue="true" 320 truevalue="true"