gatk2: depth_of_coverage.xml comparison

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

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33

author	iuc
date	Mon, 04 Jun 2018 05:38:15 -0400
parents	f244b8209eb8
children

comparison

equal deleted inserted replaced

-:84584664264c
+:35c00763cb5c
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
 <description>on BAM files</description>
-<expand macro="requirements" />
 <macros>
 <import>gatk2_macros.xml</import>
 </macros>
+<expand macro="requirements" />
+<expand macro="version_command" />
 <command interpreter="python">gatk2_wrapper.py
 ##--max_jvm_heap_fraction "1"
 --stdout "${output_log}"
-#for $i, $input_bam in enumerate( $reference_source.input_bams ):
+@BAM_INPUTS@
--d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-#if str( $input_bam.input_bam.metadata.bam_index ) != "None":
--d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
-#end if
-#end for
 -p '
 @JAR_PATH@
 -T "DepthOfCoverage"
 \$GATK2_SITE_OPTIONS
 #for $pt in str( $partition_type ).split( ',' ):
 --partitionType "${pt}"
 #end for
 #end if
 --out "${output_per_locus_coverage}"
 #for $ct_group in $summary_coverage_threshold_group:
 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
 #end for
 --outputFormat "${output_format}"
 '
 #include source=$standard_gatk_options#
 ##start analysis specific options
 #if $analysis_param_type.analysis_param_type_selector == "advanced":
 -p '
 ${analysis_param_type.ignore_deletion_sites}
 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
 #end if
 #end if
 #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 ) == "" ):
 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
 #end if
 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
 #end if
 #end if
 #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 ) == "" ):
 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
 #end if
 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
 #end if
 #end if
 </command>
 <inputs>
 <conditional name="reference_source">
 <expand macro="reference_source_selector_param" />
 <when value="cached">
-<repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
+<expand macro="input_bams_cached" />
-<param name="input_bam" type="data" format="bam" label="BAM file">
-<validator type="unspecified_build" />
-<validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-</param>
-</repeat>
 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
 <options from_data_table="gatk2_picard_indexes">
 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
 </options>
 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
 </param>
 </when>
 <when value="history"> <!-- FIX ME!!!! -->
-<repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-<param name="input_bam" type="data" format="bam" label="BAM file" />
+<expand macro="input_bams_history" />
-</repeat>
 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
 </when>
 </conditional>
 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
 <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;">
 <option value="sample" selected="True">sample</option>
 <option value="readgroup">readgroup</option>
 <option value="library">library</option>
 </param>
 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
 </repeat>
 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
 <option value="csv">csv</option>
 <option value="table">table</option>
 <option value="rtable" selected="True">rtable</option>
 </param>
 <expand macro="gatk_param_type_conditional" />
 <expand macro="analysis_type_conditional">
 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
 <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;" />
 <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;" />
 </action>
 </when>
 </conditional>
 </actions>
 </data>
 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
 <filter>'readgroup' in partition_type</filter>
 <actions>
 </action>
 </when>
 </conditional>
 </actions>
 </data>
 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
 <filter>'library' in partition_type</filter>
 <actions>
 </action>
 </when>
 </conditional>
 </actions>
 </data>
 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
 </outputs>
 <trackster_conf/>
 <tests>
 <test>
 </test>
 </tests>
 <help>
 **What it does**
 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.
 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;`_.
 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;`_.

Mercurial > repos > iuc > gatk2

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