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comparison gatk2_macros.xml @ 6:35c00763cb5c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
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5:84584664264c 6:35c00763cb5c
7 <requirement type="set_environment">GATK2_PATH</requirement> 7 <requirement type="set_environment">GATK2_PATH</requirement>
8 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement> 8 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
9 <yield /> 9 <yield />
10 </requirements> 10 </requirements>
11 </xml> 11 </xml>
12 <xml name="version_command">
13 <version_command>java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" --help|grep '^The Genome'</version_command>
14 </xml>
12 <token name="@THREADS@"> 15 <token name="@THREADS@">
13 --num_threads \${GALAXY_SLOTS:-4} 16 --num_threads \${GALAXY_SLOTS:-4}
14 </token> 17 </token>
15 <token name="@VERSION@">2.8</token> 18 <token name="@VERSION@">2.8</token>
16 <token name="@JAR_PATH@"> 19 <token name="@JAR_PATH@">
19 <token name="@DBSNP_OPTIONS@"> 22 <token name="@DBSNP_OPTIONS@">
20 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp' 23 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
21 -d "--dbsnp:${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_${dbsnp_rod_bind_type.dbsnp_rod_name}" 24 -d "--dbsnp:${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}"
22 #end if 25 #end if
23 </token> 26 </token>
27 <token name="@BAM_INPUTS@">
28 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
29 -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}"
30 #if str( $input_bam.metadata.bam_index ) != "None":
31 -d "" "${input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
32 #end if
33 #end for
34 </token>
35 <xml name="input_variants" token_help="-input,--input &amp;lt;input&amp;gt;">
36 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" multiple="True" min="1" help="@HELP@"/>
37 </xml>
38 <xml name="input_bams_history">
39 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"/>
40 </xml>
41 <xml name="input_bams_cached">
42 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
43 <validator type="unspecified_build" />
44 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
45 </param>
46 </xml>
24 <template name="standard_gatk_options"> 47 <template name="standard_gatk_options">
25 ##start standard gatk options 48 ##start standard gatk options
26 #if $gatk_param_type.gatk_param_type_selector == "advanced": 49 #if $gatk_param_type.gatk_param_type_selector == "advanced":
27 #for $pedigree in $gatk_param_type.pedigree: 50 #for $pedigree in $gatk_param_type.pedigree_files:
28 -p '--pedigree "${pedigree.pedigree_file}"' 51 -p '--pedigree "${pedigree}"'
29 #end for 52 #end for
30 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: 53 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
31 -p '--pedigreeString "${pedigree_string.pedigree_string}"' 54 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
32 #end for 55 #end for
33 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' 56 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
46 #end if 69 #end if
47 #end if 70 #end if
48 #end for 71 #end for
49 ' 72 '
50 #end for 73 #end for
51 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): 74 #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_intervals ):
52 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" 75 -d "--intervals" "${input_interval}" "${input_interval.ext}" "input_intervals_${interval_count}"
53 #end for 76 #end for
54 77
55 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): 78 #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_exclude_intervals ):
56 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" 79 -d "--excludeIntervals" "${input_interval}" "${input_interval.ext}" "input_exlude_intervals_${interval_count}"
57 #end for 80 #end for
58 81
59 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' 82 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
60 -p '--interval_padding "${gatk_param_type.interval_padding}"' 83 -p '--interval_padding "${gatk_param_type.interval_padding}"'
61 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' 84 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
79 #else 102 #else
80 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' 103 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
81 #end if 104 #end if
82 #end for 105 #end for
83 #end if 106 #end if
84 107
85 #if str( $reference_source.reference_source_selector ) == "history": 108 #if str( $reference_source.reference_source_selector ) == "history":
86 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" 109 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
87 #end if 110 #end if
88 ##end standard gatk options 111 ##end standard gatk options
89 </template> 112 </template>
95 </param> 118 </param>
96 <when value="basic"> 119 <when value="basic">
97 <!-- Do nothing here --> 120 <!-- Do nothing here -->
98 </when> 121 </when>
99 <when value="advanced"> 122 <when value="advanced">
100 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;"> 123 <param name="pedigree_files" type="data" format="txt" label="Pedigree files for samples" multiple="True" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;"/>
101 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
102 </repeat>
103 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;"> 124 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
104 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/> 125 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
105 </repeat> 126 </repeat>
106 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;"> 127 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
107 <option value="STRICT" selected="True">STRICT</option> 128 <option value="STRICT" selected="True">STRICT</option>
207 <when value="UnmappedRead"> 228 <when value="UnmappedRead">
208 <!-- no extra options --> 229 <!-- no extra options -->
209 </when> 230 </when>
210 </conditional> 231 </conditional>
211 </repeat> 232 </repeat>
212 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;"> 233 <param name="input_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;" />
213 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> 234 <param name="input_exclude_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;" />
214 </repeat> 235
215 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
216 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
217 </repeat>
218
219 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;"> 236 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
220 <option value="UNION" selected="True">UNION</option> 237 <option value="UNION" selected="True">UNION</option>
221 <option value="INTERSECTION">INTERSECTION</option> 238 <option value="INTERSECTION">INTERSECTION</option>
222 </param> 239 </param>
223 <param name="interval_padding" type="integer" value="0" min="0" label="Amount of padding (in bp) to add to each interval" 240 <param name="interval_padding" type="integer" value="0" min="0" label="Amount of padding (in bp) to add to each interval"
277 </param> 294 </param>
278 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;"> 295 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
279 <option value="ALL" selected="True">ALL</option> 296 <option value="ALL" selected="True">ALL</option>
280 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> 297 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
281 </param> 298 </param>
282 299
283 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;"> 300 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
284 <conditional name="read_group_black_list_type"> 301 <conditional name="read_group_black_list_type">
285 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> 302 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
286 <option value="file" selected="True">Filters in file</option> 303 <option value="file" selected="True">Filters in file</option>
287 <option value="text">Specify filters as a string</option> 304 <option value="text">Specify filters as a string</option>
292 <when value="text"> 309 <when value="text">
293 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> 310 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
294 </when> 311 </when>
295 </conditional> 312 </conditional>
296 </repeat> 313 </repeat>
297 314
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"/> 315 <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"/>
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"/> 316 <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"/>
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"/> 317 <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"/>
301 318
302 </when> 319 </when>
320 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> 337 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
321 <option value="cached">Locally cached</option> 338 <option value="cached">Locally cached</option>
322 <option value="history">History</option> 339 <option value="history">History</option>
323 </param> 340 </param>
324 </xml> 341 </xml>
342
343 <xml name="allow_n_cigar_reads">
344 <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue=""
345 label="Allow N in CIGAR strings" help="This is required for RNA-seq data. (-U ALLOW_N_CIGAR_READS)" />
346 </xml>
347
325 <xml name="dbsnp_param"> 348 <xml name="dbsnp_param">
326 <conditional name="dbsnp_rod_bind_type"> 349 <conditional name="dbsnp_rod_bind_type">
327 <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;"> 350 <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;">
328 <option value="set_dbsnp" selected="True">Set dbSNP</option> 351 <option value="set_dbsnp" selected="True">Set dbSNP</option>
329 <option value="exclude_dbsnp">Don't set dbSNP</option> 352 <option value="exclude_dbsnp">Don't set dbSNP</option>