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comparison gatk2_macros.xml @ 2:8bcc13094767 draft

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author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
parents 340633249b3d
children f244b8209eb8
comparison
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1:f760c0de8e3a 2:8bcc13094767
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.19">samtools</requirement> 4 <requirement type="package">gatk2</requirement>
5 <requirement type="set_environment">GATK2_PATH</requirement> 5 <requirement type="package" version="0.1.19">samtools</requirement>
6 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement> 6 <requirement type="set_environment">GATK2_PATH</requirement>
7 </requirements> 7 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
8 </xml> 8 </requirements>
9 <token name="@THREADS@"> 9 </xml>
10 --num_threads \${GALAXY_SLOTS:-4} 10 <token name="@THREADS@">
11 </token> 11 --num_threads \${GALAXY_SLOTS:-4}
12 <token name="@JAR_PATH@"> 12 </token>
13 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 13 <token name="@JAR_PATH@">
14 </token> 14 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
15 </token>
16 <token name="@DBSNP_OPTIONS@">
17 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
18 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
19 #end if
20 </token>
15 <template name="standard_gatk_options"> 21 <template name="standard_gatk_options">
16 ##start standard gatk options 22 ##start standard gatk options
17 #if $gatk_param_type.gatk_param_type_selector == "advanced": 23 #if $gatk_param_type.gatk_param_type_selector == "advanced":
18 #for $pedigree in $gatk_param_type.pedigree: 24 #for $pedigree in $gatk_param_type.pedigree:
19 -p '--pedigree "${pedigree.pedigree_file}"' 25 -p '--pedigree "${pedigree.pedigree_file}"'
309 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> 315 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
310 <option value="cached">Locally cached</option> 316 <option value="cached">Locally cached</option>
311 <option value="history">History</option> 317 <option value="history">History</option>
312 </param> 318 </param>
313 </xml> 319 </xml>
320 <xml name="dbsnp_param">
321 <conditional name="dbsnp_rod_bind_type">
322 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
323 <option value="set_dbsnp" selected="True">Set dbSNP</option>
324 <option value="exclude_dbsnp">Don't set dbSNP</option>
325 </param>
326 <when value="exclude_dbsnp" />
327 <when value="set_dbsnp">
328 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
329 <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
330 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
331 </param>
332 </when>
333 </conditional>
334 </xml>
314 <token name="@CITATION_SECTION@">------ 335 <token name="@CITATION_SECTION@">------
315 336
316 **Citation** 337 **Citation**
317 338
318 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_ 339 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_