Mercurial > repos > devteam > picard
diff picard_CollectAlignmentSummaryMetrics.xml @ 5:3d4f1fa26f0e draft
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author | devteam |
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date | Tue, 16 Dec 2014 19:03:21 -0500 |
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children | 3a3234d7a2e8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectAlignmentSummaryMetrics.xml Tue Dec 16 19:03:21 2014 -0500 @@ -0,0 +1,137 @@ +<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0"> + <description>writes a file containing summary alignment metrics</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + CollectAlignmentSummaryMetrics + INPUT="${inputFile}" + OUTPUT="${outFile}" + MAX_INSERT_SIZE=${maxinsert} + #for $sequence in $adapters: + ADAPTER_SEQUENCE="${sequence.adapter}" + #end for + METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" + IS_BISULFITE_SEQUENCED="${bisulphite}" + + REFERENCE_SEQUENCE="${reference_fasta_filename}" + + ASSUME_SORTED="${assume_sorted}" + + 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"> + </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"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing 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" size="50" 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" size="20" help="MAX_INSERT_SIZE"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + + <tests> + <test> + <param name="bisulphite" value="false" /> + <param name="sorted" value="true" /> + <param name="adaptors" value="" /> + <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 + +**Purpose** + +Reads a SAM or BAM file and writes a file containing summary alignment metrics. + +@dataset_collections@ + +@description@ + + MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with + inter-chromosomal pairs. Default value: 100000. + + ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may + be specified 0 or more times. + + METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel + LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, + LIBRARY, READ_GROUP} This option may be specified 0 or more times. + + IS_BISULFITE_SEQUENCED=Boolean + BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. + + + REFERENCE_SEQUENCE=File + R=File Reference sequence fasta Default value: null. + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. + +@more_info@ + + </help> +</tool> + +