Mercurial > repos > devteam > picard
diff picard_CollectSequencingArtifactsMetrics.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | b502c227b5e6 |
| children |
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--- a/picard_CollectSequencingArtifactsMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectSequencingArtifactsMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,112 +1,107 @@ -<tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>Collect metrics to quantify single-base sequencing artifacts</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> - </macros> - <expand macro="requirements"> - <requirement type="package" version="3.4.1">r-base</requirement> +<tool id="picard_artifact_metrics" name="Picard Collect Sequencing Artifact Metrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>Collect metrics to quantify single-base sequencing artifacts</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"> </expand> - <command detect_errors="exit_code"><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ #set $reference_fasta_filename = "localref.fa" @handle_reference_source@ - picard - CollectSequencingArtifactMetrics - I='$escaped_element_identifier' - O='OutPut' - R='${reference_fasta_filename}' - AS=${assume_sorted} - CONTEXT_SIZE=${context_size} - INCLUDE_DUPLICATES='${duplicates}' + picard CollectSequencingArtifactMetrics + --I '$escaped_element_identifier' + --O 'OutPut' + --R '${reference_fasta_filename}' + --AS ${assume_sorted} + --CONTEXT_SIZE ${context_size} + --INCLUDE_DUPLICATES '${duplicates}' #if $contexts_to_print - #for $context in str($contexts_to_print).split(','): - CONTEXTS_TO_PRINT='${context}' - #end for; + #for $context in str($contexts_to_print).split(','): + --CONTEXTS_TO_PRINT '${context}' + #end for; #end if; - MINIMUM_QUALITY_SCORE='${min_quality_score}' - INCLUDE_UNPAIRED='${unpaired}' - MAXIMUM_INSERT_SIZE='${max_size}' - MINIMUM_INSERT_SIZE='${min_size}' - MINIMUM_MAPPING_QUALITY='${minim_map_quality}' - VALIDATION_STRINGENCY='${validation_stringency}'; - ]]></command> - <inputs> - <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Load reference genome from"> - <option value="cached">Local cache</option> - <option value="history">History</option> - </param> - <when value="cached"> - <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> - <options from_data_table="picard_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + --MINIMUM_QUALITY_SCORE '${min_quality_score}' + --INCLUDE_UNPAIRED '${unpaired}' + --MAXIMUM_INSERT_SIZE '${max_size}' + --MINIMUM_INSERT_SIZE '${min_size}' + --MINIMUM_MAPPING_QUALITY '${minim_map_quality}' + --VALIDATION_STRINGENCY '${validation_stringency}'; + ]]></command> + <inputs> + <param name="inputFile" format="sam,bam" type="data" label="SAM/BAM Input file"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> + <options from_data_table="picard_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available"/> + </options> + <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/> + </when> + </conditional> + <param name="context_size" value="1" type="integer" label="How many nucleotides (context) on each side to consider" help="e.g NXN corresponds to 1 "N" on each side of "X""/> + <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts"> + <sanitizer> + <valid initial="string.letters"> + <add value=","/> + </valid> + </sanitizer> </param> - </when> - <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> - </when> - </conditional> - - <param name='context_size' value="1" type='integer' label='How many nucleotides (context) on each side to consider' help='e.g NXN corresponds to 1 "N" on each side of "X"'/> - <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts"> - <sanitizer> - <valid initial="string.letters"><add value="," /></valid> - </sanitizer> - </param> - <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/> - <param name="max_size" type="integer" value="600" label="Maximum insert size"/> - <param name="min_size" type="integer" value="30" label="Minimum insert size"/> - <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/> - <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/> - <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/> - <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/> - - <expand macro="VS" /> - - </inputs> - - <outputs> - <data name='pre_details' format="tabular" from_work_dir="OutPut.pre_adapter_detail_metrics" label='Detailed table for artifacts introduced prior to the addition of adapters'/> - <data name='pre_summary' format="tabular" from_work_dir="OutPut.pre_adapter_summary_metrics" label='Summary table for artifacts introduced prior to the addition of adapters'/> - <data name='pos_details' format="tabular" from_work_dir="OutPut.bait_bias_detail_metrics" label='Detailed table for artifacts introduced posterior to the addition of adapters'/> - <data name='pos_summary' format="tabular" from_work_dir="OutPut.bait_bias_summary_metrics" label='Summary table for artifacts introduced posterior to the addition of adapters'/> - <data name='err_summary' format="tabular" from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/> - </outputs> - - <tests> - <test> - <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" /> - <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="picard_BedToIntervalList_ref.fa" /> - <param name="context_size" value="1" /> - <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" /> - <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/> - <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/> - <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/> - <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/> - <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/> - </test> - <test> - <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/> - <param name="reference_source_selector" value="cached"/> - <param name="context_size" value="1" /> - <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" /> - <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/> - <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/> - <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/> - <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/> - <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/> - </test> - </tests> - <help> + <param name="min_quality_score" type="integer" value="30" label="Minimum base quality score"/> + <param name="max_size" type="integer" value="600" label="Maximum insert size"/> + <param name="min_size" type="integer" value="30" label="Minimum insert size"/> + <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/> + <param name="assume_sorted" type="boolean" label="Assume SAM/BAM is sorted"/> + <param name="duplicates" type="boolean" label="Include duplicates" checked="false" truevalue="true" falsevalue="false"/> + <param name="unpaired" type="boolean" label="Include unpaired reads" checked="false" truevalue="true" falsevalue="false"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data name="pre_details" format="tabular" from_work_dir="OutPut.pre_adapter_detail_metrics" label="Detailed table for artifacts introduced prior to the addition of adapters"/> + <data name="pre_summary" format="tabular" from_work_dir="OutPut.pre_adapter_summary_metrics" label="Summary table for artifacts introduced prior to the addition of adapters"/> + <data name="pos_details" format="tabular" from_work_dir="OutPut.bait_bias_detail_metrics" label="Detailed table for artifacts introduced posterior to the addition of adapters"/> + <data name="pos_summary" format="tabular" from_work_dir="OutPut.bait_bias_summary_metrics" label="Summary table for artifacts introduced posterior to the addition of adapters"/> + <data name="err_summary" format="tabular" from_work_dir="OutPut.error_summary_metrics" label="General Summary of artifactual errors"/> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam"/> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_BedToIntervalList_ref.fa"/> + <param name="context_size" value="1"/> + <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/> + <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/> + <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/> + <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/> + <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/> + <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/> + </test> + <test> + <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/> + <param name="reference_source_selector" value="cached"/> + <param name="context_size" value="1"/> + <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/> + <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/> + <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/> + <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/> + <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/> + <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/> + </test> + </tests> + <help> .. class:: infomark @@ -145,5 +140,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>