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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
comparison
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5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0"> 1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
2 <description>on BAM files</description> 2 <description>on BAM files</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python">gatk2_wrapper.py 8 <command interpreter="python">gatk2_wrapper.py
8 ##--max_jvm_heap_fraction "1" 9 ##--max_jvm_heap_fraction "1"
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 #for $i, $input_bam in enumerate( $reference_source.input_bams ): 11 @BAM_INPUTS@
11 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
12 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
13 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
14 #end if
15 #end for
16 -p ' 12 -p '
17 @JAR_PATH@ 13 @JAR_PATH@
18 -T "DepthOfCoverage" 14 -T "DepthOfCoverage"
19 \$GATK2_SITE_OPTIONS 15 \$GATK2_SITE_OPTIONS
20 16
30 #for $pt in str( $partition_type ).split( ',' ): 26 #for $pt in str( $partition_type ).split( ',' ):
31 --partitionType "${pt}" 27 --partitionType "${pt}"
32 #end for 28 #end for
33 #end if 29 #end if
34 --out "${output_per_locus_coverage}" 30 --out "${output_per_locus_coverage}"
35 31
36 #for $ct_group in $summary_coverage_threshold_group: 32 #for $ct_group in $summary_coverage_threshold_group:
37 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}" 33 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
38 #end for 34 #end for
39 --outputFormat "${output_format}" 35 --outputFormat "${output_format}"
40 ' 36 '
41 37
42 #include source=$standard_gatk_options# 38 #include source=$standard_gatk_options#
43 ##start analysis specific options 39 ##start analysis specific options
44 #if $analysis_param_type.analysis_param_type_selector == "advanced": 40 #if $analysis_param_type.analysis_param_type_selector == "advanced":
45 -p ' 41 -p '
46 ${analysis_param_type.ignore_deletion_sites} 42 ${analysis_param_type.ignore_deletion_sites}
82 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": 78 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
83 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample} 79 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
84 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample} 80 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
85 #end if 81 #end if
86 #end if 82 #end if
87 83
88 #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 ) == "" ): 84 #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 ) == "" ):
89 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": 85 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
90 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} 86 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
91 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} 87 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
92 #end if 88 #end if
101 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": 97 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
102 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup} 98 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
103 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup} 99 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
104 #end if 100 #end if
105 #end if 101 #end if
106 102
107 #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 ) == "" ): 103 #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 ) == "" ):
108 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": 104 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
109 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library} 105 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
110 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} 106 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
111 #end if 107 #end if
120 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": 116 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
121 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library} 117 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
122 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library} 118 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
123 #end if 119 #end if
124 #end if 120 #end if
125
126 121
127 </command> 122 </command>
128 <inputs> 123 <inputs>
129 <conditional name="reference_source"> 124 <conditional name="reference_source">
130 <expand macro="reference_source_selector_param" /> 125 <expand macro="reference_source_selector_param" />
131 <when value="cached"> 126 <when value="cached">
132 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 127 <expand macro="input_bams_cached" />
133 <param name="input_bam" type="data" format="bam" label="BAM file">
134 <validator type="unspecified_build" />
135 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
136 </param>
137 </repeat>
138 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 128 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
139 <options from_data_table="gatk2_picard_indexes"> 129 <options from_data_table="gatk2_picard_indexes">
140 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 130 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
141 </options> 131 </options>
142 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 132 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
143 </param> 133 </param>
144 </when> 134 </when>
145 <when value="history"> <!-- FIX ME!!!! --> 135 <when value="history"> <!-- FIX ME!!!! -->
146 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 136
147 <param name="input_bam" type="data" format="bam" label="BAM file" /> 137 <expand macro="input_bams_history" />
148 </repeat>
149 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 138 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
150 </when> 139 </when>
151 </conditional> 140 </conditional>
152 141
153 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" /> 142 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
154 143
155 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;gt;"> 144 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;gt;">
156 <option value="sample" selected="True">sample</option> 145 <option value="sample" selected="True">sample</option>
157 <option value="readgroup">readgroup</option> 146 <option value="readgroup">readgroup</option>
158 <option value="library">library</option> 147 <option value="library">library</option>
159 </param> 148 </param>
160 149
161 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;"> 150 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
162 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" /> 151 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
163 </repeat> 152 </repeat>
164 153
165 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" > 154 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
166 <option value="csv">csv</option> 155 <option value="csv">csv</option>
167 <option value="table">table</option> 156 <option value="table">table</option>
168 <option value="rtable" selected="True">rtable</option> 157 <option value="rtable" selected="True">rtable</option>
169 </param> 158 </param>
170 159
171 <expand macro="gatk_param_type_conditional" /> 160 <expand macro="gatk_param_type_conditional" />
172 161
173 <expand macro="analysis_type_conditional"> 162 <expand macro="analysis_type_conditional">
174 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" /> 163 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
175 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" /> 164 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
176 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &amp;lt;maxBaseQuality&amp;gt;" /> 165 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &amp;lt;maxBaseQuality&amp;gt;" />
177 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &amp;lt;minBaseQuality&amp;gt;" /> 166 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &amp;lt;minBaseQuality&amp;gt;" />
356 </action> 345 </action>
357 </when> 346 </when>
358 </conditional> 347 </conditional>
359 </actions> 348 </actions>
360 </data> 349 </data>
361 350
362 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" > 351 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
363 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> 352 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
364 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> 353 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
365 <filter>'readgroup' in partition_type</filter> 354 <filter>'readgroup' in partition_type</filter>
366 <actions> 355 <actions>
509 </action> 498 </action>
510 </when> 499 </when>
511 </conditional> 500 </conditional>
512 </actions> 501 </actions>
513 </data> 502 </data>
514 503
515 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" > 504 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
516 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> 505 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
517 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> 506 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
518 <filter>'library' in partition_type</filter> 507 <filter>'library' in partition_type</filter>
519 <actions> 508 <actions>
662 </action> 651 </action>
663 </when> 652 </when>
664 </conditional> 653 </conditional>
665 </actions> 654 </actions>
666 </data> 655 </data>
667 656
668 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" /> 657 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
669 </outputs> 658 </outputs>
670 <trackster_conf/> 659 <trackster_conf/>
671 <tests> 660 <tests>
672 <test> 661 <test>
688 </test> 677 </test>
689 </tests> 678 </tests>
690 <help> 679 <help>
691 **What it does** 680 **What it does**
692 681
693 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. 682 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.
694 683
695 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html&gt;`_. 684 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html&gt;`_.
696 685
697 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_. 686 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
698 687