gatk2: depth_of_coverage.xml annotate

annotate depth_of_coverage.xml @ 8:3012e466d7fc draft default tip

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit bb4bc974dacb3db49db5f22d937f520bdddd9190

author	sanbi-uwc
date	Tue, 29 May 2018 05:56:19 -0400
parents	6e985e2e0802
children

rev	line source
0 6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	2 <description>on BAM files</description>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	3 <macros>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	4 <import>gatk2_macros.xml</import>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	5 </macros>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	6 <expand macro="requirements" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	7 <expand macro="version_command" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	8 <command interpreter="python">gatk2_wrapper.py
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	9 ##--max_jvm_heap_fraction "1"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	10 --stdout "${output_log}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	11 @BAM_INPUTS@
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	12 -p '
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	13 @JAR_PATH@
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	14 -T "DepthOfCoverage"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	15 \$GATK2_SITE_OPTIONS
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	16
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	17 @THREADS@
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	18
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	19 @INTERVAL_STATS@
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	20
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	21 #if $reference_source.reference_source_selector != "history":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	22 -R "${reference_source.ref_file.fields.path}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	23 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	24 #if str( $input_calculate_coverage_over_genes ) != "None":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	25 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	26 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	27 #if str( $partition_type ) != "None":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	28 #for $pt in str( $partition_type ).split( ',' ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	29 --partitionType "${pt}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	30 #end for
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	31 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	32 --out "${output_per_locus_coverage}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	33
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	34 #for $ct_group in $summary_coverage_threshold_group:
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	35 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	36 #end for
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	37 --outputFormat "${output_format}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	38 '
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	39
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	40 #include source=$standard_gatk_options#
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	41 ##start analysis specific options
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	42 #if $analysis_param_type.analysis_param_type_selector == "advanced":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	43 -p '
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	44 ${analysis_param_type.ignore_deletion_sites}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	45 ${analysis_param_type.include_deletions}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	46 --maxBaseQuality "${analysis_param_type.max_base_quality}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	47 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	48 --minBaseQuality "${analysis_param_type.min_base_quality}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	49 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	50 --nBins "${analysis_param_type.n_bins}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	51 ${analysis_param_type.omit_depth_output_at_each_base}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	52 ${analysis_param_type.omit_interval_statistics}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	53 ${analysis_param_type.omit_locus_table}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	54 ${analysis_param_type.omit_per_sample_stats}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	55 ${analysis_param_type.print_base_counts}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	56 ${analysis_param_type.print_bin_endpoints_and_exit}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	57 --start "${analysis_param_type.start}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	58 --stop "${analysis_param_type.stop}"
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	59 '
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	60 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	61 ##Move additional files to final location
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	62 #if str( $partition_type ) != "None":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	63 #set $partition_types = str( $partition_type ).split( ',' )
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	64 #else:
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	65 #set $partition_types = [ 'sample' ]
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	66 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	67 #if 'sample' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	68 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	69 && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	70 && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	71 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	72 #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	73 && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	74 && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	75 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	76 #if str( $input_calculate_coverage_over_genes ) != "None":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	77 && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	78 && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	79 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	80 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	81 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	82 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	83 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	84 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	85
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	86 #if 'readgroup' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	87 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	88 && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	89 && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	90 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	91 #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	92 && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	93 && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	94 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	95 #if str( $input_calculate_coverage_over_genes ) != "None":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	96 && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	97 && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	98 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	99 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	100 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	101 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	102 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	103 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	104
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	105 #if 'library' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	106 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	107 && mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	108 && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	109 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	110 #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ):
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	111 && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	112 && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	113 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	114 #if str( $input_calculate_coverage_over_genes ) != "None":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	115 && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	116 && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	117 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	118 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	119 && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	120 && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	121 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	122 #end if
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	123
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	124 </command>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	125 <inputs>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	126 <conditional name="reference_source">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	127 <expand macro="reference_source_selector_param" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	128 <when value="cached">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	129 <expand macro="input_bams_cached" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	130 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	131 <options from_data_table="gatk2_picard_indexes">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	132 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	133 </options>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	134 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	135 </param>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	136 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	137 <when value="history"> <!-- FIX ME!!!! -->
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	138 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &lt;input_file&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	139 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	140 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	141 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	142
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	143 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	144
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	145 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &lt;partitionType&gt;">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	146 <option value="sample" selected="True">sample</option>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	147 <option value="readgroup">readgroup</option>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	148 <option value="library">library</option>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	149 </param>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	150
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	151 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	152 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	153 </repeat>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	154
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	155 <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	156 <option value="csv">csv</option>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	157 <option value="table">table</option>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	158 <option value="rtable" selected="True">rtable</option>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	159 </param>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	160
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	161 <expand macro="gatk_param_type_conditional" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	162
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	163 <expand macro="analysis_type_conditional">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	164 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	165 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	166 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &lt;maxBaseQuality&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	167 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &lt;minBaseQuality&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	168 <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &lt;maxMappingQuality&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	169 <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &lt;minMappingQuality&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	170 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &lt;nBins&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	171 <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	172 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	173 <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	174 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	175 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	176 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	177 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	178 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	179 </expand>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	180 </inputs>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	181 <outputs>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	182 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	183 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	184 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	185 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	186 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	187 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	188 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	189 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	190 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	191 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	192 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	193 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	194 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	195 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	196 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	197 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	198 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	199 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	200 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	201 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	202 <filter>'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	203 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	204 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	205 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	206 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	207 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	208 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	209 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	210 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	211 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	212 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	213 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	214 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	215 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	216 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	217 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	218 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	219 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	220 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	221 <filter>'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	222 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	223 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	224 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	225 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	226 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	227 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	228 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	229 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	230 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	231 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	232 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	233 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	234 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	235 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	236 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	237 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	238 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	239 <filter>'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	240 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	241 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	242 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	243 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	244 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	245 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	246 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	247 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	248 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	249 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	250 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	251 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	252 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	253 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	254 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	255 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	256 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	257 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	258 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	259 <filter>'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	260 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	261 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	262 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	263 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	264 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	265 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	266 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	267 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	268 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	269 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	270 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	271 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	272 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	273 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	274 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	275 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	276 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	277 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	278 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	279 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	280 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	281 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	282 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	283 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	284 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	285 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	286 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	287 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	288 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	289 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	290 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	291 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	292 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	293 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	294 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	295 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	296 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	297 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	298 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	299 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	300 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	301 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	302 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	303 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	304 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	305 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	306 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	307 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	308 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	309 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	310 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	311 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	312 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	313 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	314 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	315 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	316 <filter>'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	317 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	318 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	319 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	320 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	321 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	322 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	323 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	324 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	325 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	326 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	327 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	328 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	329 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	330 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	331 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	332 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	333 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	334 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	335 <filter>'sample' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	336 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	337 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	338 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	339 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	340 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	341 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	342 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	343 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	344 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	345 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	346 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	347 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	348 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	349 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	350 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	351
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	352 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	353 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	354 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	355 <filter>'readgroup' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	356 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	357 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	358 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	359 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	360 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	361 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	362 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	363 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	364 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	365 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	366 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	367 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	368 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	369 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	370 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	371 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	372 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	373 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	374 <filter>'readgroup' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	375 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	376 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	377 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	378 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	379 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	380 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	381 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	382 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	383 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	384 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	385 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	386 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	387 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	388 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	389 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	390 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	391 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	392 <filter>'readgroup' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	393 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	394 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	395 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	396 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	397 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	398 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	399 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	400 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	401 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	402 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	403 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	404 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	405 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	406 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	407 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	408 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	409 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	410 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	411 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	412 <filter>'readgroup' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	413 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	414 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	415 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	416 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	417 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	418 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	419 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	420 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	421 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	422 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	423 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	424 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	425 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	426 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	427 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	428 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	429 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	430 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	431 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	432 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	433 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	434 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	435 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	436 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	437 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	438 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	439 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	440 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	441 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	442 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	443 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	444 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	445 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	446 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	447 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	448 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	449 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	450 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	451 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	452 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	453 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	454 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	455 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	456 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	457 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	458 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	459 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	460 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	461 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	462 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	463 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	464 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	465 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	466 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	467 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	468 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	469 <filter>'readgroup' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	470 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	471 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	472 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	473 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	474 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	475 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	476 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	477 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	478 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	479 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	480 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	481 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	482 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	483 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	484 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	485 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	486 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	487 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	488 <filter>'readgroup' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	489 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	490 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	491 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	492 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	493 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	494 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	495 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	496 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	497 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	498 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	499 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	500 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	501 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	502 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	503 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	504
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	505 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	506 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	507 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	508 <filter>'library' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	509 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	510 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	511 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	512 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	513 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	514 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	515 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	516 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	517 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	518 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	519 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	520 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	521 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	522 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	523 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	524 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	525 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	526 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	527 <filter>'library' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	528 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	529 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	530 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	531 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	532 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	533 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	534 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	535 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	536 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	537 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	538 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	539 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	540 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	541 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	542 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	543 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	544 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	545 <filter>'library' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	546 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	547 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	548 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	549 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	550 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	551 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	552 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	553 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	554 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	555 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	556 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	557 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	558 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	559 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	560 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	561 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	562 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	563 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	564 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	565 <filter>'library' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	566 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	567 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	568 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	569 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	570 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	571 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	572 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	573 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	574 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	575 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	576 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	577 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	578 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	579 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	580 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	581 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	582 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	583 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	584 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	585 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	586 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	587 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	588 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	589 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	590 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	591 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	592 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	593 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	594 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	595 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	596 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	597 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	598 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	599 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	600 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	601 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	602 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	603 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	604 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	605 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	606 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	607 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	608 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	609 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	610 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	611 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	612 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	613 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	614 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	615 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	616 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	617 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	618 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	619 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	620 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	621 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	622 <filter>'library' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	623 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	624 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	625 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	626 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	627 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	628 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	629 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	630 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	631 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	632 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	633 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	634 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	635 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	636 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	637 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	638 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	639 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	640 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	641 <filter>'library' in partition_type</filter>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	642 <actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	643 <conditional name="output_format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	644 <when value="rtable">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	645 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	646 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	647 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	648 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	649 <when value="csv">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	650 <action type="format">
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	651 <option type="from_param" name="output_format" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	652 </action>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	653 </when>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	654 </conditional>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	655 </actions>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	656 </data>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	657
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	658 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	659 </outputs>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	660 <trackster_conf/>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	661 <tests>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	662 <test>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	663 <param name="reference_source_selector" value="history" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	664 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	665 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	666 <param name="input_calculate_coverage_over_genes" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	667 <param name="partition_type" value="sample" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	668 <param name="summary_coverage_threshold_group" value="0" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	669 <param name="output_format" value="rtable" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	670 <param name="gatk_param_type_selector" value="basic" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	671 <param name="analysis_param_type_selector" value="basic" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	672 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	673 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	674 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	675 <output name="output_cumulative_coverage_counts_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_cumulative_coverage_counts_sample.tabular" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	676 <output name="output_cumulative_coverage_proportions_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_output_cumulative_coverage_proportions_sample.tabular" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	677 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	678 </test>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	679 </tests>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	680 <help>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	681 What it does
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	682
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	683 DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	684
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	685 For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	686
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	687 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	688
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	689 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	690
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	691 ------
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	692
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	693 Inputs
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	694
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	695 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	696
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	697
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	698 Outputs
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	699
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	700 The output is in various table formats.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	701
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	702
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	703 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	704
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	705 -------
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	706
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	707 Settings::
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	708
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	709 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	710 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	711 includeDeletions boolean false Include information on deletions
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	712 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	713 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	714 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	715 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	716 nBins int 499 Number of bins to use for granular binning
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	717 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	718 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	719 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	720 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	721 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	722 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	723 printBaseCounts boolean false Will add base counts to per-locus output.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	724 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	725 start int 1 Starting (left endpoint) for granular binning
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	726 stop int 500 Ending (right endpoint) for granular binning
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	727 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	728
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	729 @CITATION_SECTION@
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	730 </help>
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	731 <expand macro="citations" />
6e985e2e0802 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204 sanbi-uwc parents: diff changeset	732 </tool>

Mercurial > repos > sanbi-uwc > gatk2

annotate depth_of_coverage.xml @ 8:3012e466d7fc draft default tip