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comparison gatk2_macros.xml @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 8bcc13094767
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package">gatk2</requirement> 4 <requirement type="package">gatk2</requirement>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 <requirement type="package" version="0.1.19">samtools</requirement>
6 <requirement type="package" version="1.56.0">picard</requirement>
6 <requirement type="set_environment">GATK2_PATH</requirement> 7 <requirement type="set_environment">GATK2_PATH</requirement>
7 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement> 8 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
9 <yield />
8 </requirements> 10 </requirements>
9 </xml> 11 </xml>
10 <token name="@THREADS@"> 12 <token name="@THREADS@">
11 --num_threads \${GALAXY_SLOTS:-4} 13 --num_threads \${GALAXY_SLOTS:-4}
12 </token> 14 </token>
15 <token name="@VERSION@">2.8</token>
13 <token name="@JAR_PATH@"> 16 <token name="@JAR_PATH@">
14 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 17 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
15 </token> 18 </token>
16 <token name="@DBSNP_OPTIONS@"> 19 <token name="@DBSNP_OPTIONS@">
17 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp' 20 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
52 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): 55 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
53 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" 56 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
54 #end for 57 #end for
55 58
56 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' 59 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
57 60 -p '--interval_padding "${gatk_param_type.interval_padding}"'
58 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' 61 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
59 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": 62 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
60 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' 63 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
61 #end if 64 #end if
62 -p ' 65 -p '
215 218
216 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;"> 219 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
217 <option value="UNION" selected="True">UNION</option> 220 <option value="UNION" selected="True">UNION</option>
218 <option value="INTERSECTION">INTERSECTION</option> 221 <option value="INTERSECTION">INTERSECTION</option>
219 </param> 222 </param>
220 223 <param name="interval_padding" type="integer" value="0" min="0" label="Amount of padding (in bp) to add to each interval"
224 help="This is typically used to add padding around exons when analyzing exomes. (--interval_padding / -ip)"/>
225
221 <conditional name="downsampling_type"> 226 <conditional name="downsampling_type">
222 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;"> 227 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
223 <option value="NONE" selected="True">NONE</option> 228 <option value="NONE" selected="True">NONE</option>
224 <option value="ALL_READS">ALL_READS</option> 229 <option value="ALL_READS">ALL_READS</option>
225 <option value="BY_SAMPLE">BY_SAMPLE</option> 230 <option value="BY_SAMPLE">BY_SAMPLE</option>
293 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> 298 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
294 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/> 299 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
295 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/> 300 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
296 301
297 </when> 302 </when>
298 </conditional> 303 </conditional>
299 </xml> 304 </xml>
300 <xml name="analysis_type_conditional"> 305 <xml name="analysis_type_conditional">
301 <conditional name="analysis_param_type"> 306 <conditional name="analysis_param_type">
302 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> 307 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
303 <option value="basic" selected="True">Basic</option> 308 <option value="basic" selected="True">Basic</option>
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;`_ 344 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;`_
340 345
341 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* 346 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
342 347
343 </token> 348 </token>
349 <xml name="citations">
350 <citations>
351 <citation type="doi">10.1038/ng.806</citation>
352 <citation type="doi">10.1101/gr.107524.110</citation>
353 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
354 </citations>
355 </xml>
344 </macros> 356 </macros>