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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
| author | yhoogstrate |
|---|---|
| date | Wed, 07 Oct 2015 11:36:27 -0400 |
| parents | b486372c8948 |
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<tool id="featurecounts" name="featureCounts" version="1.4.6.p5"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> <requirement type="package" version="1.4.6.p5">featurecounts</requirement> </requirements> <version_command>featureCounts -v 2>&1 | grep .</version_command> <command><![CDATA[ ## Check 01: do the alignments have a dbkey and is the option set to using it? #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/gene_sets.loc' is configured properly!" >&2 #else ## Check 02: are all alignments from the same type (bam || sam) #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1 echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&2 #else featureCounts -a #if $reference_gene_sets_source.source_select == "indexed_filtered" "$reference_gene_sets_source.reference_gene_sets" #else if $reference_gene_sets_source.source_select == "indexed_all" "$reference_gene_sets_source.reference_gene_sets" #else if $reference_gene_sets_source.source_select == "history" "$reference_gene_sets_source.reference_gene_sets" #else #* This is a workaround to obtain the "genome.fa" file that corresponds to the dbkey of the alignments. Because this file is "calculated" during run-time, it can be used in a workflow. *# "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }" #end if -o "${output}" -T \${GALAXY_SLOTS:-2} #if $extended_parameters.parameters == "extended" -t $extended_parameters.gff_feature_type -g $extended_parameters.gff_feature_attribute $extended_parameters.summarization_level $extended_parameters.contribute_to_multiple_features $extended_parameters.protocol $extended_parameters.multimapping_counts -Q $extended_parameters.mapping_quality $extended_parameters.fragment_counting $extended_parameters.check_distance -d $extended_parameters.minimum_fragment_length -D $extended_parameters.maximum_fragment_length $extended_parameters.only_both_ends $extended_parameters.exclude_chimerics #end if #for $alignment in $alignments ${alignment} #end for 2>&1 #set $columns = [str(i+7) for i, alignment in enumerate($alignments)] #set $columns=",".join($columns) #if $format == "tabdel_default" or $format.value == "tabdel_default" && cp $output tmp.txt && egrep -v "^#" tmp.txt > tmp2.txt && cut -f 1,$columns tmp2.txt > tmp_left.txt && cut -f 6 tmp2.txt > tmp_right.txt && paste tmp_left.txt tmp_right.txt > $output #elif $format == "tabdel_short" or $format.value == "tabdel_short" && cp $output tmp.txt && egrep -v "^#" tmp.txt | cut -f 1,$columns > $output #end if ## For every alignment, replace its filename for: "hid: sample name" #for $alignment in $alignments #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.') #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/') #if $format.value == "tabdel_default" or $format.value == "tabdel_short" && sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt #elif $format.value == "bed": && $__tool_directory__/featurecounts2bed.sh -f "$output" > tmp.txt #else && sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt #end if && mv tmp.txt "${output}" && sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt && mv tmp.txt ${output}".summary" #end for && mv ${output}".summary" "${output_summary}" #end if #end if ]]></command> <inputs> <param name="alignments" type="data" 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 in the series must be in THE SAME format." multiple="true" /> <!-- Find out how to access the the GTF/GFF file(s) --> <conditional name="reference_gene_sets_source"> <param name="source_select" type="select" label="GFF/GTF Source"> <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> <option value="history">Use reference from the history</option> <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option> <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option> </param> <when value="indexed_filtered"> <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> <column name="name" index="0"/> <column name="dbkey" index="1"/> <column name="value" index="2"/> <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" /> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> </when> <when value="history"> <param name="reference_gene_sets" format="gff" 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." /> </when> <when value="indexed_all"> <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> <column name="name" index="0"/> <column name="dbkey" index="1"/> <column name="value" index="2"/> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> </when> <when value="attribute"> <!-- Do nothing, determine GTF/GFF file at runtime --> </when> </conditional> <param name="format" type="select" label="Output format"> <option value="tabdel_default">Gene-name "\t" gene-count "\t" gene-length</option> <option value="tabdel_short" selected="true">Gene-name "\t" gene-count</option> <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount</option> <option value="complex">featureCounts 1.4.0+ default (extensive; complex)</option> </param> <conditional name="extended_parameters"> <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings."> <option value="default">Default settings</option> <option value="extended">Extended settings</option> </param> <when value="default"> </when> <when value="extended"> <param name="gff_feature_type" type="text" value="exon" 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" 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 ="contribute_to_multiple_features" type="boolean" truevalue=" -O" falsevalue="" label="Allow read to contribute to multiple features" help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" /> <param name="protocol" type="select" label="Strand specific protocol" help="Indicate if strand-specific read counting should be performed."> <option value=" -s 0" selected="true">Unstranded</option> <option value=" -s 1">Stranded (forwards)</option> <option value=" -s 2">Stranded (reverse)</option> </param> <param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue="" label="Count multi-mapping reads/fragments" help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads." /> <param name="mapping_quality" type="integer" value="12" label="Minimum read quality" 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. 12 by default." /> <param name="fragment_counting" type="boolean" truevalue=" -p" falsevalue="" checked="true" label="PE: Count fragments instead of reads" help="Paired-end specific: If specified, fragments (or templates) will be counted instead of reads." /> <param name="check_distance" type="boolean" truevalue=" -P" falsevalue="" label="PE: Check paired-end distance" help="Paired-end specific: 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." /> <param name="minimum_fragment_length" type="integer" value="50" label="PE: Minimum fragment/template length." /> <param name="maximum_fragment_length" type="integer" value="600" label="PE: Maximum fragment/template length." /> <param name="only_both_ends" type="boolean" truevalue=" -B" falsevalue="" label="PE: only allow fragments with both reads aligned" help="Paired-end specific: 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="" checked="true" label="PE: Exclude chimeric fragments" help="Paired-end specific: 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." /> <param name ="summarization_level" type="boolean" truevalue=" -f" falsevalue="" 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." /> </when> </conditional> </inputs> <outputs> <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" /> </outputs> <tests> <test> <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" /> <param name="source_select" value="history" /> <param name="format" value="tabdel_default" /> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> <output name="output" file="output.tab"/> <output name="output_summary" file="output_summary.tab"/> </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. It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1]. Input formats ------------- Alignments should be provided in either: - SAM format, http://samtools.sourceforge.net/samtools.shtml#5 - BAM format 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 Installation ------------ 1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history. 2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at: https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables License ------- **featureCounts / subread package**: - GNU General Public License version 3.0 (GPLv3) Contact ------- The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds: http://toolshed.g2.bx.psu.edu/ http://testtoolshed.g2.bx.psu.edu/ References ---------- **featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.** *Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30. - http://www.ncbi.nlm.nih.gov/pubmed/24227677 - http://dx.doi.org/10.1093/bioinformatics/btt656 Acknowledgements ---------------- I would like to thank Marius van den Beek for his contribution to this galaxy wrapper. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btt656</citation> </citations> </tool>