Mercurial > repos > iuc > gatk2
diff gatk2_macros.xml @ 6:35c00763cb5c draft default tip
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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--- a/gatk2_macros.xml Mon Aug 25 17:44:53 2014 -0400 +++ b/gatk2_macros.xml Mon Jun 04 05:38:15 2018 -0400 @@ -9,6 +9,9 @@ <yield /> </requirements> </xml> + <xml name="version_command"> + <version_command>java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" --help|grep '^The Genome'</version_command> + </xml> <token name="@THREADS@"> --num_threads \${GALAXY_SLOTS:-4} </token> @@ -21,11 +24,31 @@ -d "--dbsnp:${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}" #end if </token> + <token name="@BAM_INPUTS@"> + #for $i, $input_bam in enumerate( $reference_source.input_bams ): + -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}" + #if str( $input_bam.metadata.bam_index ) != "None": + -d "" "${input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index + #end if + #end for + </token> + <xml name="input_variants" token_help="-input,--input &lt;input&gt;"> + <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" multiple="True" min="1" help="@HELP@"/> + </xml> + <xml name="input_bams_history"> + <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &lt;input_file&gt;"/> + </xml> + <xml name="input_bams_cached"> + <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &lt;input_file&gt;"> + <validator type="unspecified_build" /> + <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 --> + </param> + </xml> <template name="standard_gatk_options"> ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $pedigree in $gatk_param_type.pedigree: - -p '--pedigree "${pedigree.pedigree_file}"' + #for $pedigree in $gatk_param_type.pedigree_files: + -p '--pedigree "${pedigree}"' #end for #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: -p '--pedigreeString "${pedigree_string.pedigree_string}"' @@ -48,12 +71,12 @@ #end for ' #end for - #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): - -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_intervals ): + -d "--intervals" "${input_interval}" "${input_interval.ext}" "input_intervals_${interval_count}" #end for - - #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): - -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + + #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_exclude_intervals ): + -d "--excludeIntervals" "${input_interval}" "${input_interval.ext}" "input_exlude_intervals_${interval_count}" #end for -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' @@ -81,7 +104,7 @@ #end if #end for #end if - + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -97,9 +120,7 @@ <!-- Do nothing here --> </when> <when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/> - </repeat> + <param name="pedigree_files" type="data" format="txt" label="Pedigree files for samples" multiple="True" help="-ped,--pedigree &lt;pedigree&gt;"/> <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"> <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/> </repeat> @@ -209,13 +230,9 @@ </when> </conditional> </repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"> - <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> - </repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"> - <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> - </repeat> - + <param name="input_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;" /> + <param name="input_exclude_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;" /> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"> <option value="UNION" selected="True">UNION</option> <option value="INTERSECTION">INTERSECTION</option> @@ -279,7 +296,7 @@ <option value="ALL" selected="True">ALL</option> <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> </param> - + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"> <conditional name="read_group_black_list_type"> <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> @@ -294,7 +311,7 @@ </when> </conditional> </repeat> - + <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"/> <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"/> <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"/> @@ -322,6 +339,12 @@ <option value="history">History</option> </param> </xml> + + <xml name="allow_n_cigar_reads"> + <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue="" + label="Allow N in CIGAR strings" help="This is required for RNA-seq data. (-U ALLOW_N_CIGAR_READS)" /> + </xml> + <xml name="dbsnp_param"> <conditional name="dbsnp_rod_bind_type"> <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &lt;dbsnp&gt;">