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Changeset 11:83312f73e0e7 (2019-06-01)

Previous changeset 10:c9ede7ae3ac1 (2019-06-01) Next changeset 12:7b2f77e2b0a4 (2019-06-01)

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added:
gatk2_macros.xml

diff -r c9ede7ae3ac1 -r 83312f73e0e7 gatk2_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gatk2_macros.xml Sat Jun 01 07:11:19 2019 -0400

[

b'@@ -0,0 +1,379 @@\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package">gatk2</requirement>\n+ <requirement type="package" version="0.1.19">samtools</requirement>\n+ <requirement type="package" version="1.56.0">picard</requirement>\n+ <requirement type="set_environment">GATK2_PATH</requirement>\n+ <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command>java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" --help|grep \'^The Genome\'</version_command>\n+ </xml>\n+ <token name="@THREADS@">\n+ --num_threads \\${GALAXY_SLOTS:-4}\n+ </token>\n+ <token name="@VERSION@">2.8</token>\n+ <token name="@JAR_PATH@">\n+ java -jar "\\$GATK2_PATH/GenomeAnalysisTK.jar"\n+ </token>\n+ <token name="@DBSNP_OPTIONS@">\n+ #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == \'set_dbsnp\'\n+ -d "--dbsnp:${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}"\n+ #end if\n+ </token>\n+ <token name="@BAM_INPUTS@">\n+ #for $i, $input_bam in enumerate( $reference_source.input_bams ):\n+ -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}"\n+ #if str( $input_bam.metadata.bam_index ) != "None":\n+ -d "" "${input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index\n+ #end if\n+ #end for\n+ </token>\n+ <xml name="input_variants" token_help="-input,--input &lt;input&gt;">\n+ <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" multiple="True" min="1" help="@HELP@"/>\n+ </xml>\n+ <xml name="input_bams_history">\n+ <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &lt;input_file&gt;"/>\n+ </xml>\n+ <xml name="input_bams_cached">\n+ <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &lt;input_file&gt;">\n+ <validator type="unspecified_build" />\n+ <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." /> \n+ </param>\n+ </xml>\n+ <template name="standard_gatk_options">\n+ ##start standard gatk options\n+ #if $gatk_param_type.gatk_param_type_selector == "advanced":\n+ #for $pedigree in $gatk_param_type.pedigree_files:\n+ -p \'--pedigree "${pedigree}"\'\n+ #end for\n+ #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:\n+ -p \'--pedigreeString "${pedigree_string.pedigree_string}"\'\n+ #end for\n+ -p \'--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"\'\n+ #set default_read_filters = [\'MalformedRead\']\n+ #for $read_filter in $gatk_param_type.read_filter:\n+ -p \'\n+ #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:\n+ --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"\n+ #end if\n+ #for $name, $param in $read_filter.read_filter_type.iteritems():\n+ #if $name not in [ "__current_case__", "read_filter_type_selector" ]:\n+ #if hasattr( $param.input, \'truevalue\' ):\n+ ${param}\n+ #else:\n+ --${name} "${param}"\n+ #end if\n+ #end if\n+ #end for\n+ \'\n+ #end for\n+ #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_intervals ):\n+ -d "--intervals" "${input_interval}" "${input_interval.ext}" "input_intervals_${interv'..b'name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />\n+ </when>\n+ </conditional>\n+ </repeat>\n+\n+ <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"/>\n+ <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"/>\n+ <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"/>\n+\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="analysis_type_conditional">\n+ <conditional name="analysis_param_type">\n+ <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">\n+ <option value="basic" selected="True">Basic</option>\n+ <option value="advanced">Advanced</option>\n+ </param>\n+ <when value="basic">\n+ \n+ </when>\n+ <when value="advanced">\n+ <yield />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="reference_source_selector_param">\n+ <param name="reference_source_selector" type="select" label="Choose the source for the reference list">\n+ <option value="cached">Locally cached</option>\n+ <option value="history">History</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="allow_n_cigar_reads">\n+ <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue=""\n+ label="Allow N in CIGAR strings" help="This is required for RNA-seq data. (-U ALLOW_N_CIGAR_READS)" />\n+ </xml>\n+\n+ <xml name="dbsnp_param">\n+ <conditional name="dbsnp_rod_bind_type">\n+ <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &lt;dbsnp&gt;">\n+ <option value="set_dbsnp" selected="True">Set dbSNP</option>\n+ <option value="exclude_dbsnp">Don\'t set dbSNP</option>\n+ </param>\n+ <when value="exclude_dbsnp" />\n+ <when value="set_dbsnp">\n+ <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />\n+ <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">\n+ <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\\w+$</validator>\n+ </param>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@CITATION_SECTION@">------\n+\n+**Citation**\n+\n+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. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_\n+\n+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n+\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/ng.806</citation>\n+ <citation type="doi">10.1101/gr.107524.110</citation>\n+ <citation type="doi">10.1002/0471250953.bi1110s43</citation>\n+ </citations>\n+ </xml>\n+</macros>\n'