Mercurial > repos > devteam > picard
diff picard_CollectAlignmentSummaryMetrics.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 | f9242e01365a |
| children |
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--- a/picard_CollectAlignmentSummaryMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectAlignmentSummaryMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,11 +1,11 @@ -<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>writes a file containing summary alignment metrics</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ +<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>writes a file containing summary alignment metrics</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ ##set up input files @@ -14,79 +14,77 @@ @handle_reference_source@ - picard - CollectAlignmentSummaryMetrics - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" - MAX_INSERT_SIZE=${maxinsert} + picard CollectAlignmentSummaryMetrics + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --MAX_INSERT_SIZE ${maxinsert} #for $sequence in $adapters: - ADAPTER_SEQUENCE="${sequence.adapter}" + --ADAPTER_SEQUENCE '${sequence.adapter}' #end for #for $level in str($metric_accumulation_level).split(','): - METRIC_ACCUMULATION_LEVEL="${level}" + --METRIC_ACCUMULATION_LEVEL '${level}' #end for - IS_BISULFITE_SEQUENCED="${bisulphite}" + --IS_BISULFITE_SEQUENCED '${bisulphite}' - REFERENCE_SEQUENCE="${reference_fasta_filename}" + --REFERENCE_SEQUENCE '${reference_fasta_filename}' - ASSUME_SORTED="${assume_sorted}" + --ASSUME_SORTED '${assume_sorted}' - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]></command> - <inputs> - <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> - <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="Using reference genome" help="REFERENCE_SEQUENCE"> - <options from_data_table="all_fasta"> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> + <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="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + <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"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/> + </when> + </conditional> + <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> + <option value="ALL_READS" selected="True">All reads</option> + <option value="SAMPLE">Sample</option> + <option value="LIBRARY">Library</option> + <option value="READ_GROUP">Read group</option> </param> - </when> - <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> - </when> - </conditional> - <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> - <option value="ALL_READS" selected="True">All reads</option> - <option value="SAMPLE">Sample</option> - <option value="LIBRARY">Library</option> - <option value="READ_GROUP">Read group</option> - </param> - <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> - <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> - <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> - <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> - </repeat> - <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> - <expand macro="VS" /> - - </inputs> - <outputs> - <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tablular"/> - </outputs> - <tests> - <test> - <param name="bisulphite" value="false" /> - <param name="assume_sorted" value="true" /> - <repeat name="adapters"> - <param name="adapter" value = ""/> - </repeat> - <param name="maxinsert" value="100000" /> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" value="picard_CASM_ref.fa" /> - <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> - <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> - </test> - </tests> - <help> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> + <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> + <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> + </repeat> + <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> + </outputs> + <tests> + <test> + <param name="bisulphite" value="false"/> + <param name="assume_sorted" value="true"/> + <repeat name="adapters"> + <param name="adapter" value=""/> + </repeat> + <param name="maxinsert" value="100000"/> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_CASM_ref.fa"/> + <param name="inputFile" value="picard_CASM.bam" ftype="bam"/> + <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + <help> .. class:: infomark @@ -121,5 +119,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>