Mercurial > repos > iuc > featurecounts
changeset 30:56aa64c23690 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Tue, 31 Aug 2021 08:07:43 +0000 |
| parents | 3cd88f5c9d4c |
| children | 83ab9e468b86 |
| files | featurecounts.xml featurecounts.xml.orig |
| diffstat | 2 files changed, 647 insertions(+), 10 deletions(-) [+] |
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--- a/featurecounts.xml Mon Aug 30 13:47:16 2021 +0000 +++ b/featurecounts.xml Tue Aug 31 08:07:43 2021 +0000 @@ -1,10 +1,12 @@ <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> - <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> + <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> <macros> <token name="@TOOL_VERSION@">2.0.1</token> <token name="@VERSION_SUFFIX@">1</token> </macros> - + <xrefs> + <xref type="bio.tools">subread</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">subread</requirement> <requirement type="package" version="1.11">samtools</requirement> @@ -281,8 +283,8 @@ <conditional name = "multifeatures"> <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction"> - <option value="" selected="true">Disabled: reads that align to multiple features or overlapping features are excluded</option> - <option value="-M">Enabled: multi-mapping reads are included (-M)</option> + <option value="" selected="true">Disabled; reads that align to multiple features or overlapping features are excluded</option> + <option value="-M">Enabled; multi-mapping reads are included (-M)</option> <option value="-O">Enabled: multi-overlapping features are included (-O)</option> <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option> </param> @@ -293,8 +295,8 @@ truevalue="--fraction" falsevalue="" argument="--fraction" - label="Assign fractions to multi-mapping reads" - help="If specified, a fractional count 1/x will be generated for each multi-mapping read, where x is the number of alignments (indicated by 'NH' tag) reported for the read."/> + label="Assign fractions to multimapping reads" + help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> </when> <when value="-O"> <param name="fraction" @@ -302,8 +304,8 @@ truevalue="--fraction" falsevalue="" argument="--fraction" - label="Assign fractions to multi-overlapping features" - help="If specified, a fractional count 1/y will be generated for each multi-overlapping feature, where y is the number of features overlapping with the read."/> + label="Assign fractions to multimapping reads" + help="If specified, a fractional count 1/n will be generated for each multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> </when> <when value="-O -M"> <param name="fraction" @@ -311,8 +313,8 @@ truevalue="--fraction" falsevalue="" argument="--fraction" - label="Assign fractions to both multi-mapping reads and multi-overlapping features" - help="If specified, a fractional count 1/(x*y) will be generated, where x is the number of alignments (indicated by 'NH' tag) and y the number of overlapping features."/> + label="Assign fractions to multimapping reads" + help="If specified, a fractional count 1/n will be generated for each multi-mapping or multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> </when> </conditional>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featurecounts.xml.orig Tue Aug 31 08:07:43 2021 +0000 @@ -0,0 +1,635 @@ +<<<<<<< HEAD +<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> + <macros> + <token name="@TOOL_VERSION@">2.0.1</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> + +======= +<tool id="featurecounts" name="featureCounts" version="2.0.1" profile="16.04"> + <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> + <xrefs> + <xref type='bio.tools'>subread</xref> + </xrefs> +>>>>>>> d0c3b656f (add bio.tools ID) + <requirements> + <requirement type="package" version="@TOOL_VERSION@">subread</requirement> + <requirement type="package" version="1.11">samtools</requirement> + <requirement type="package" version="8.31">coreutils</requirement> + </requirements> + + <version_command>featureCounts -v 2>&1 | grep .</version_command> + <command detect_errors="exit_code"><![CDATA[ + + ## Export fc path for its built-in annotation + + export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && + + ## Check whether all alignments are from the same type (bam || sam) + featureCounts + + #if $anno.anno_select=="history": + -a '$anno.reference_gene_sets' + -F "GTF" + #elif $anno.anno_select=="cached": + -a '$anno.reference_gene_sets_builtin.fields.path' + -F "GTF" + #elif $anno.anno_select=="builtin": + -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt + -F "SAF" + #end if + + -o "output" + -T \${GALAXY_SLOTS:-2} + + -s $strand_specificity + -t '$extended_parameters.gff_feature_type' + -g '$extended_parameters.gff_feature_attribute' + $extended_parameters.summarization_level + + $extended_parameters.multifeatures.multifeat + #if $extended_parameters.multifeatures.multifeat != "": + $extended_parameters.multifeatures.fraction + #end if + + + ## $extended_parameters.contribute_to_multiple_features + ## $extended_parameters.multimapping_enabled.multimapping_counts + + ###if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M": + ## $extended_parameters.multimapping_enabled.fraction + ###end if --> + + $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads + #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": + #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome: + -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' + #end if + #end if + + $extended_parameters.long_reads + + $extended_parameters.by_read_group + + -Q $extended_parameters.mapping_quality + $extended_parameters.largest_overlap + --minOverlap $extended_parameters.min_overlap + --fracOverlap $extended_parameters.frac_overlap + --fracOverlapFeature $extended_parameters.frac_overlap_feature + $extended_parameters.read_reduction + $extended_parameters.primary + $extended_parameters.ignore_dup + #if $extended_parameters.R: + $extended_parameters.R + #end if + #if str($extended_parameters.read_extension_5p) != "0": + --readExtension5 $extended_parameters.read_extension_5p + #end if + + #if str($extended_parameters.read_extension_3p) != "0": + --readExtension3 $extended_parameters.read_extension_3p + #end if + + $pe_parameters.fragment_counting_enabled.fragment_counting + #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p": + $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance + #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P": + -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length + -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length + #end if + #end if + + $pe_parameters.only_both_ends + $pe_parameters.exclude_chimerics + + '${alignment}' + + ## Remove comment and add sample name to header + && grep -v "^#" "output" + | sed -e 's|${alignment}|${alignment.element_identifier}|g' + > body.txt + ## Set the right columns for the tabular formats + #if $format.value == "tabdel_medium": + && cut -f 1,7 body.txt > expression_matrix.txt + + ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8 + ## Thus the gene length column (last column) has to be added separately + && cut -f 6 body.txt > gene_lengths.txt + && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak + && mv -f expression_matrix.txt.bak '${output_medium}' + #elif $format.value == "tabdel_short": + && cut -f 1,7 body.txt > '${output_short}' + #else: + && cp body.txt '${output_full}' + #end if + + #if str($include_feature_length_file) == "true": + && cut -f 1,6 body.txt > '${output_feature_lengths}' + #end if + + #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": + && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' + #end if + + #if $extended_parameters.R: + && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam + #end if + && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' + ]]></command> + <inputs> + <param name="alignment" + type="data" + multiple="false" + format="bam,sam" + label="Alignment file" + help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" > + </param> + + <param name="strand_specificity" + type="select" + label="Specify strand information" + argument="-s" + help="Indicate if the data is stranded and if strand-specific read counting should be performed. Strand setting must be the same as the strand settings used to produce the mapped BAM input(s)"> + <option value="0" selected="true">Unstranded</option> + <option value="1">Stranded (Forward)</option> + <option value="2">Stranded (Reverse)</option> + </param> + + <conditional name="anno"> + <param name="anno_select" type="select" label="Gene annotation file"> + <option value="builtin">featureCounts built-in</option> + <option value="cached" selected="True">locally cached</option> + <option value="history">in your history</option> + </param> + <when value="builtin"> + <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts"> + <options from_data_table="featurecounts_anno"> + <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/> + </options> + </param> + </when> + <when value="cached"> + <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator"> + <options from_data_table="gene_sets"> + <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/> + <filter type="sort_by" column="2" /> + </options> + <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="reference_gene_sets" + format="gff,gtf,gff3" + type="data" + label="Gene annotation file" + help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment"> + </param> + </when> + </conditional> + + <param name="format" + type="select" + label="Output format" + help="The output format will be tabular, select the preferred columns here"> + <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option> + <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option> + <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option> + </param> + + <param name="include_feature_length_file" + type="boolean" + truevalue="true" + falsevalue="false" + checked="false" + label="Create gene-length file" + help="Creates a tabular file that contains the effective (nucleotides used for counting reads) length of the feature; might be useful for estimating FPKM/RPKM" /> + + + <section name="pe_parameters" title="Options for paired-end reads"> + <conditional name="fragment_counting_enabled"> + + <param name="fragment_counting" + type="select" + argument="-p" + checked="true" + label="Count fragments instead of reads" + help="If specified, fragments (or templates) will be counted instead of reads."> + <option value="" selected="true">Disabled; all reads/mates will be counted individually</option> + <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option> + </param> + + <when value=" -p"> + <conditional name="check_distance_enabled"> + <param name="check_distance" + type="boolean" + truevalue=" -P" + falsevalue="" + argument="-P" + label="Check paired-end distance" + help="If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." /> + <when value=" -P"> + <param name="minimum_fragment_length" + type="integer" + value="50" + argument="-d" + label="Minimum fragment/template length." /> + <param name="maximum_fragment_length" + type="integer" + value="600" + argument="-D" + label="Maximum fragment/template length." /> + </when> + <when value="" /> + </conditional> + </when> + <when value="" /> + </conditional> + + <param name="only_both_ends" + type="boolean" + truevalue=" -B" + falsevalue="" + argument="-B" + label="Only allow fragments with both reads aligned" + help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." /> + + <param name="exclude_chimerics" + type="boolean" + truevalue=" -C" + falsevalue="" + argument="-C" + checked="true" + label="Exclude chimeric fragments" + help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." /> + </section> + + <section name="extended_parameters" title="Advanced options"> + <param name="gff_feature_type" + type="text" + value="exon" + argument="-t" + label="GFF feature type filter" + help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default." /> + + <param name="gff_feature_attribute" + type="text" + value="gene_id" + argument="-g" + label="GFF gene identifier" + help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization." /> + + <param name="summarization_level" + type="boolean" + truevalue=" -f" + falsevalue="" + argument="-f" + label="On feature level" + help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." /> + + <conditional name = "multifeatures"> + <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction"> + <option value="" selected="true">Disabled; reads that align to multiple features or overlapping features are excluded</option> + <option value="-M">Enabled; multi-mapping reads are included (-M)</option> + <option value="-O">Enabled: multi-overlapping features are included (-O)</option> + <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option> + </param> + <when value=""/> + <when value="-M"> + <param name="fraction" + type="boolean" + truevalue="--fraction" + falsevalue="" + argument="--fraction" + label="Assign fractions to multimapping reads" + help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> + </when> + <when value="-O"> + <param name="fraction" + type="boolean" + truevalue="--fraction" + falsevalue="" + argument="--fraction" + label="Assign fractions to multimapping reads" + help="If specified, a fractional count 1/n will be generated for each multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> + </when> + <when value="-O -M"> + <param name="fraction" + type="boolean" + truevalue="--fraction" + falsevalue="" + argument="--fraction" + label="Assign fractions to multimapping reads" + help="If specified, a fractional count 1/n will be generated for each multi-mapping or multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> + </when> + </conditional> + + <param name="mapping_quality" + type="integer" + value="0" + argument="-Q" + label="Minimum mapping quality per read" + help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." /> + + <conditional name="exon_exon_junction_read_counting_enabled"> + <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue="" + label="Exon-exon junctions" + help="If specified, reads supporting each exon-exon junction will be counted" /> + <when value="-J"> + <param name="genome" argument="-G" type="data" format="fasta" optional="true" + label="Reference sequence file" + help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" /> + </when> + <when value="" /> + </conditional> + + <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" + label="Long reads" + help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." /> + + <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue="" + label="Count reads by read group" + help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." /> + + + <param name="largest_overlap" + type="boolean" + truevalue=" --largestOverlap" + falsevalue="" + argument="--largestOverlap" + label="Largest overlap" + help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases" /> + + <param name="min_overlap" + type="integer" + value="1" + argument="--minOverlap" + label="Minimum bases of overlap" + help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." /> + + <param name="frac_overlap" + type="integer" + value="0" + min="0" + max="1" + argument="--fracOverlap" + label="Minimum fraction (of read) overlapping a feature" + help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." /> + + <param name="frac_overlap_feature" + type="integer" + value="0" + min="0" + max="1" + argument="--fracOverlapFeature" + label="Minimum fraction (of feature) overlapping a read" + help="Specify the minimum required fraction of bases included in a feature overlapping bases between a read (or a read-pair). Value should be within range [0,1]. 0 by default." /> + + <param name="read_extension_5p" + type="integer" + value="0" + argument="--readExtension5" + label="Read 5' extension" + help="Reads are extended upstream by ... bases from their 5' end" /> + + <param name="read_extension_3p" + type="integer" + value="0" + argument="--readExtension3" + label="Read 3' extension" + help="Reads are extended upstream by ... bases from their 3' end" /> + + <param name="read_reduction" + type="select" + label="Reduce read to single position" + argument="--read2pos" + help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on the single base the the read is reduced to."> + <option value="" selected="true">Leave the read as it is</option> + <option value="--read2pos 5">Reduce it to the 5' end</option> + <option value="--read2pos 3">Reduce it to the 3' end</option> + </param> + + <param name="primary" + type="boolean" + truevalue=" --primary" + falsevalue="" + argument="--primary" + label="Only count primary alignments" + help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." /> + + <param name="ignore_dup" + type="boolean" + truevalue=" --ignoreDup" + falsevalue="" + argument="--ignoreDup" + label="Ignore reads marked as duplicate" + help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> + + <param type="boolean" + truevalue="-R BAM" + falsevalue="" + argument="-R" + label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)." + help="" /> + + <param name="count_split_alignments_only" + type="boolean" + truevalue=" --countSplitAlignmentsOnly" + falsevalue="" + argument="--countSplitAlignmentsOnly" + label="Ignore unspliced alignments" + help="If specified, only split alignments (CIGAR strings containing the letter `N') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." /> + </section> + </inputs> + <outputs> + <data format="tabular" + name="output_medium" + label="${tool.name} on ${on_string}: Counts (with length)"> + <filter>format == "tabdel_medium"</filter> + <actions> + <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" /> + </actions> + </data> + + <data format="bam" + name="output_bam" + label="${tool.name} on ${on_string}: Alignment file"> + <filter>extended_parameters['R']</filter> + </data> + + <data format="tabular" + name="output_short" + label="${tool.name} on ${on_string}: Counts"> + <filter>format == "tabdel_short"</filter> + <actions> + <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" /> + </actions> + </data> + + <data format="tabular" + name="output_full" + label="${tool.name} on ${on_string}: Counts (with location)"> + <filter>format == "tabdel_full"</filter> + <actions> + <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" /> + </actions> + </data> + + <data format="tabular" + name="output_summary" + label="${tool.name} on ${on_string}: Summary"> + <actions> + <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" /> + </actions> + </data> + + <data format="tabular" + name="output_feature_lengths" + label="${tool.name} on ${on_string}: Feature lengths"> + <filter>include_feature_length_file</filter> + <actions> + <action name="column_names" type="metadata" default="Feature,Length" /> + </actions> + </data> + + <data name="output_jcounts" format="tabular" + label="${tool.name} on ${on_string}: Junction counts"> + <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter> + <actions> + <action name="column_names" type="metadata" + default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" /> + </actions> + </data> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> + <param name="anno_select" value="history"/> + <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" /> + <param name="format" value="tabdel_medium" /> + <param name="include_feature_length_file" value="true"/> + <output name="output_medium" file="output_1_medium.tab"> + <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> + </output> + <output name="output_summary" file="output_1_summary.tab"> + <metadata name="column_names" value="Status,featureCounts_input1.bam"/> + </output> + </test> + <test expect_num_outputs="3"> + <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> + <param name="anno_select" value="history"/> + <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" /> + <param name="format" value="tabdel_full" /> + <param name="include_feature_length_file" value="true"/> + <output name="output_full" file="output_1_full.tab"> + <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/> + </output> + <output name="output_summary" file="output_1_summary.tab"> + <metadata name="column_names" value="Status,featureCounts_input1.bam"/> + </output> + <output name="output_feature_lengths" file="output_feature_lengths.tab"> + <metadata name="column_names" value="Feature,Length"/> + </output> + </test> + <test expect_num_outputs="4"> + <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> + <param name="anno_select" value="history"/> + <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" /> + <param name="format" value="tabdel_short" /> + <param name="include_feature_length_file" value="true"/> + <param name="count_exon_exon_junction_reads" value="-J"/> + <output name="output_short" file="output_1_short.tab"> + <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> + </output> + <output name="output_summary" file="output_1_summary.tab"> + <metadata name="column_names" value="Status,featureCounts_input1.bam"/> + </output> + <output name="output_jcounts" file="output_1_jcounts.tab"> + <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> + </output> + </test> + <!-- Ensure featureCounts built-in annotation works --> + <test expect_num_outputs="3"> + <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" /> + <param name="anno_select" value="builtin"/> + <param name="format" value="tabdel_short" /> + <section name="extended_parameters"> + <param name="R" value="true" /> + </section> + <output name="output_short" file="output_builtin_hg19.tab"> + <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + </output> + <output name="output_summary" file="output_summary_builtin_hg19.tab"/> + <output name="output_bam" file="output.bam" ftype="bam"/> + </test> + <!-- Ensure cached GTFs work --> + <test expect_num_outputs="3"> + <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> + <param name="anno_select" value="cached"/> + <param name="format" value="tabdel_medium" /> + <param name="include_feature_length_file" value="true"/> + <output name="output_medium" file="output_1_medium.tab"> + <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> + </output> + <output name="output_summary" file="output_1_summary.tab"> + <metadata name="column_names" value="Status,featureCounts_input1.bam"/> + </output> + </test> + <!-- Ensure BAM output works --> + <test> + <param name="alignment" value="subset.sorted.bam" ftype="bam" /> + <param name="anno_select" value="history" /> + <param name="reference_gene_sets" value="small.gtf" ftype="gtf" /> + <section name="extended_parameters" > + <param name="R" value="true" /> + </section> + <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +featureCounts +############# + +Overview +-------- +FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files. FeatureCounts is part of the Subread_ package. + +Input formats +------------- +Alignments should be provided in either: + + - SAM format, http://samtools.sourceforge.net/samtools.shtml#5 + - BAM format + +Annotations for gene regions should be provided in the GFF/GTF format: + + - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 + - http://www.ensembl.org/info/website/upload/gff.html + +Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These annotation files are in simplified annotation format (SAF) as shown below. The GeneID column contains Entrez gene identifiers and each entry (row) is taken as a feature (e.g. an exon). + +Example - **Built-in annotation format**: + + ====== ==== ======= ======= ====== + GeneID Chr Start End Strand + ====== ==== ======= ======= ====== + 497097 chr1 3204563 3207049 - + 497097 chr1 3411783 3411982 - + 497097 chr1 3660633 3661579 - + ====== ==== ======= ======= ====== + +These annotation files can be found in the `Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool. + +Output format +------------- +FeatureCounts produces a table containing counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2, edgeR and limma-voom Galaxy wrappers by IUC. + +.. _Subread: http://subread.sourceforge.net/ +.. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf +.. _`Subread package`: https://sourceforge.net/projects/subread/files/ + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt656</citation> + </citations> +</tool>