Mercurial > repos > devteam > picard
diff picard_CollectRnaSeqMetrics.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 |
line wrap: on
line diff
--- a/picard_CollectRnaSeqMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectRnaSeqMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ -<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> +<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.4.1">r-base</requirement> - <requirement type="package" version="357">ucsc-gff3togenepred</requirement> - <requirement type="package" version="357">ucsc-gtftogenepred</requirement> + <requirement type="package" version="447">ucsc-gff3togenepred</requirement> + <requirement type="package" version="447">ucsc-gtftogenepred</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ ## Set up input files @@ -35,159 +34,138 @@ ## Start picard command @java_options@ - picard - CollectRnaSeqMetrics - REF_FLAT=refFlat.tab + picard CollectRnaSeqMetrics + --REF_FLAT refFlat.tab #if str( $ribosomal_intervals ) != "None": - RIBOSOMAL_INTERVALS="${ribosomal_intervals}" + --RIBOSOMAL_INTERVALS '${ribosomal_intervals}' #end if - STRAND_SPECIFICITY="${strand_specificity}" - MINIMUM_LENGTH="${minimum_length}" - CHART_OUTPUT="${pdfFile}" + --STRAND_SPECIFICITY '${strand_specificity}' + --MINIMUM_LENGTH '${minimum_length}' + --CHART_OUTPUT '${pdfFile}' #for $sequence_to_ignore in $ignore_list: - IGNORE_SEQUENCE="${sequence_to_ignore.sequence}" + --IGNORE_SEQUENCE '${sequence_to_ignore.sequence}' #end for - RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}" - METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" - REFERENCE_SEQUENCE="${reference_fasta_filename}" - ASSUME_SORTED="${assume_sorted}" - VALIDATION_STRINGENCY=${validation_stringency} + --RRNA_FRAGMENT_PERCENTAGE '${rrna_fragment_percentage}' + --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}' + --INPUT '$escaped_element_identifier' + -OUTPUT '${outFile}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ASSUME_SORTED '${assume_sorted}' + --VALIDATION_STRINGENCY ${validation_stringency} ]]></command> - - <inputs> - <param format="sam,bam" type="data" name="inputFile" 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"/> + <inputs> + <param format="sam,bam" type="data" name="inputFile" 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"/> + <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> + <conditional name="gene_reference_source"> + <param name="gene_reference_source_selector" type="select" label="Load gene annotation from"> + <option value="gtf">GTF/GFF3</option> + <option value="refflat">refFlat</option> </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> - - <conditional name="gene_reference_source"> - <param name="gene_reference_source_selector" type="select" label="Load gene annotation from"> - <option value="gtf">GTF/GFF3</option> - <option value="refflat">refFlat</option> - </param> - <when value="gtf"> - <param name="refFlat" - format="gtf,gff3" - type="data" - label="Gene annotation (GTF/GFF3)"/> - </when> - <when value="refflat"> - <param name="refFlat" - format="tabular" - type="data" - label="Gene annotations in refFlat form" - help="See "Obtaining gene annotations in refFlat format" below for help"/> - </when> - </conditional> - - - <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/> - <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand."> - <option value="NONE" selected="True">None</option> - <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> - <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option> - </param> - <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/> - <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below"> - <param name="sequence" type="text" label="Ignore reads matching this sequence"/> - </repeat> - <param name="rrna_fragment_percentage" type="float" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA." help="RRNA_FRAGMENT_PERCENTAGE; default=0.8"/> - <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"/> - - <expand macro="VS" /> - - </inputs> - <outputs> - <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> - <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> - </outputs> - - <tests> - <test> - <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> - <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> - <param name="assume_sorted" value="true" /> - - <param name="gene_reference_source_selector" value="refflat" /> - <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> - <param name="metric_accumulation_level" value="ALL_READS" /> - <param name="minimum_length" value="500" /> - <param name="strand_specificity" value="NONE" /> - <param name="rrna_fragment_percentage" value="0.8" /> - <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> - </test> - <test> - <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> - <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> - <param name="assume_sorted" value="true" /> - - <param name="gene_reference_source_selector" value="refflat" /> - <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output" /> - <param name="metric_accumulation_level" value="ALL_READS" /> - <param name="minimum_length" value="500" /> - <param name="strand_specificity" value="NONE" /> - <param name="rrna_fragment_percentage" value="0.8" /> - <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> - </test> - - <test> - <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> - <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> - <param name="assume_sorted" value="true" /> - - <param name="gene_reference_source_selector" value="gtf" /> - <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" /> - <param name="metric_accumulation_level" value="ALL_READS" /> - <param name="minimum_length" value="500" /> - <param name="strand_specificity" value="NONE" /> - <param name="rrna_fragment_percentage" value="0.8" /> - <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/> - </test> - - <test> - <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> - <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> - <param name="assume_sorted" value="true" /> - - <param name="gene_reference_source_selector" value="gtf" /> - <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" /> - <param name="metric_accumulation_level" value="ALL_READS" /> - <param name="minimum_length" value="500" /> - <param name="strand_specificity" value="NONE" /> - <param name="rrna_fragment_percentage" value="0.8" /> - <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/> - </test> - </tests> - <help> + <when value="gtf"> + <param name="refFlat" format="gtf,gff3" type="data" label="Gene annotation (GTF/GFF3)"/> + </when> + <when value="refflat"> + <param name="refFlat" format="tabular" type="data" label="Gene annotations in refFlat form" help="See "Obtaining gene annotations in refFlat format" below for help"/> + </when> + </conditional> + <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/> + <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand."> + <option value="NONE" selected="True">None</option> + <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> + <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option> + </param> + <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/> + <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below"> + <param name="sequence" type="text" label="Ignore reads matching this sequence"/> + </repeat> + <param name="rrna_fragment_percentage" type="float" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA." help="RRNA_FRAGMENT_PERCENTAGE; default=0.8"/> + <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"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> + <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> + <param name="assume_sorted" value="true"/> + <param name="gene_reference_source_selector" value="refflat"/> + <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat"/> + <param name="metric_accumulation_level" value="ALL_READS"/> + <param name="minimum_length" value="500"/> + <param name="strand_specificity" value="NONE"/> + <param name="rrna_fragment_percentage" value="0.8"/> + <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + <test> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> + <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> + <param name="assume_sorted" value="true"/> + <param name="gene_reference_source_selector" value="refflat"/> + <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output"/> + <param name="metric_accumulation_level" value="ALL_READS"/> + <param name="minimum_length" value="500"/> + <param name="strand_specificity" value="NONE"/> + <param name="rrna_fragment_percentage" value="0.8"/> + <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + <test> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> + <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> + <param name="assume_sorted" value="true"/> + <param name="gene_reference_source_selector" value="gtf"/> + <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf"/> + <param name="metric_accumulation_level" value="ALL_READS"/> + <param name="minimum_length" value="500"/> + <param name="strand_specificity" value="NONE"/> + <param name="rrna_fragment_percentage" value="0.8"/> + <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/> + </test> + <test> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> + <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> + <param name="assume_sorted" value="true"/> + <param name="gene_reference_source_selector" value="gtf"/> + <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3"/> + <param name="metric_accumulation_level" value="ALL_READS"/> + <param name="minimum_length" value="500"/> + <param name="strand_specificity" value="NONE"/> + <param name="rrna_fragment_percentage" value="0.8"/> + <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + <help> .. class:: infomark @@ -265,5 +243,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>