featurecounts: featurecounts.xml comparison

comparison featurecounts.xml @ 10:7d1e37c6ef85 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8

author	iuc
date	Sun, 14 Jan 2018 09:23:33 -0500
parents	81e9f94f257c
children	d0beb2753aba

comparison

equal deleted inserted replaced

-:81e9f94f257c
+:7d1e37c6ef85
-<tool id="featurecounts" name="featureCounts" version="1.6.0.1" profile="16.04">
+<tool id="featurecounts" name="featureCounts" version="1.6.0.2" profile="16.04">
 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
 <requirements>
 <requirement type="package" version="1.6.0">subread</requirement>
 </requirements>
 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
-<command><![CDATA[
+<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 $gtf_source.ref_source=="history":
--a '$gtf_source.reference_gene_sets'
+#if $anno.anno_select=="gtf":
-#else:
+#if $anno.gtf_source.ref_source=="history":
--a '$gtf_source.reference_gene_sets_builtin.fields.path'
+-a '$anno.gtf_source.reference_gene_sets'
+#else:
+-a '$anno.gtf_source.reference_gene_sets_builtin.fields.path'
+#end if
+-F "GTF"
+#elif $anno.anno_select=="builtin":
+-a \${FC_PATH}/annotation/${anno.genome}_RefSeq_exon.txt
+-F "SAF"
 #end if
 -o "output"
 -T \${GALAXY_SLOTS:-2}
 $extended_parameters.summarization_level
 $extended_parameters.contribute_to_multiple_features
 -s  $extended_parameters.strand_specificity
 $extended_parameters.multimapping_enabled.multimapping_counts
-#if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M"
+#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 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
+#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
 --fracOverlapFeature $extended_parameters.frac_overlap_feature
 $extended_parameters.read_reduction
 $extended_parameters.primary
 $extended_parameters.ignore_dup
-#if str($extended_parameters.read_extension_5p) != "0"
+#if str($extended_parameters.read_extension_5p) != "0":
 --readExtension5 $extended_parameters.read_extension_5p
 #end if
-#if str($extended_parameters.read_extension_3p) != "0"
+#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"
+#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"
+#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}'
-## Removal of comment and column-header line
+## Removal of comment
-&& grep -v "^#" "output" | tail -n+2 > body.txt
+&& grep -v "^#" "output"
+#if $format.value != "tabdel_short":
+## and remove column-header line
+| tail -n+2
+#else
+## update header
+| sed --expression='s|${alignment}|${alignment.element_identifier}|g'
+#end if
+> body.txt
 ## Set the right columns for the tabular formats
-#if $format.value == "tabdel_medium"
+#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"
+#elif $format.value == "tabdel_short" or $format.value == "tabdel_short_noheader":
 && cut -f 1,7 body.txt > '${output_short}'
-#else
+#else:
 && cp body.txt '${output_full}'
 #end if
+#if str($include_feature_length_file) == "true":
-#if str($include_feature_length_file) == "true"
 && cut -f 1,6 body.txt > '${output_feature_lengths}'
 #end if
-#if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
+#if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
-&& tail -n+2 'output.jcounts' > '${output_jcounts}'
+#if $format.value != "tabdel_short":
+&& tail -n+2 'output.jcounts' > '${output_jcounts}'
+#else:
+&& sed --expression='s|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
+#end if
 #end if
-&& tail -n+2 'output.summary' > '${output_summary}'
+#if $format.value != "tabdel_short":
+&& tail -n+2 'output.summary' > '${output_summary}'
+#else:
+&& sed --expression='s|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
+#end if
 ]]></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" />
+<conditional name="anno">
-<conditional name="gtf_source">
+<param name="anno_select" type="select" label="Gene annotation file">
-<param name="ref_source" type="select" label="Gene annotation file">
+<option value="builtin">featureCounts built-in</option>
-<option value="cached">locally cached</option>
+<option value="gtf">GTF file</option>
-<option value="history">in your history</option>
 </param>
-<when value="cached">
+<when value="builtin">
-<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">
+<param name="genome" 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="gene_sets">
+<option value="hg38">hg38</option>
-<filter type="sort_by" column="1" />
+<option value="hg19">hg19</option>
-<validator type="no_options" message="No annotations are available." />
+<option value="mm10">mm10</option>
-</options>
+<option value="mm9">mm9</option>
 </param>
 </when>
-<when value="history">
+<when value="gtf">
-<param name="reference_gene_sets"
+<conditional name="gtf_source">
-format="gff,gtf,gff3"
+<param name="ref_source" type="select" label="Gene annotation file">
-type="data"
+<option value="cached">locally cached</option>
-label="Gene annotation file"
+<option value="history">in your history</option>
-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 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="sort_by" column="1" />
+<validator type="no_options" message="No annotations are available." />
+</options>
+</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" />
+</when>
+</conditional>
 </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" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
+<option value="tabdel_short_noheader" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
+<option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/edgeR/limma-voom compatible, includes header in output)</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"
 <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"
 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"
 </data>
 <data format="tabular"
 name="output_short"
 label="${tool.name} on ${on_string}">
-<filter>format == "tabdel_short"</filter>
+<filter>format == "tabdel_short_noheader" or format == "tabdel_short"</filter>
 <actions>
 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" />
 </actions>
 </data>
 </actions>
 </data>
 <data format="tabular"
 name="output_summary"
-hidden="true"
 label="${tool.name} on ${on_string}: summary">
 <actions>
 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
 </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}" />
+<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="4">
 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+<param name="anno_select" value="gtf"/>
 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
-<param name="format" value="tabdel_short" />
+<param name="format" value="tabdel_short_noheader" />
 <param name="include_feature_length_file" value="true"/>
 <param name="ref_source" value="history" />
 <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"/>
 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
 </output>
 </test>
 <test expect_num_outputs="3">
 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+<param name="anno_select" value="gtf"/>
 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
 <param name="format" value="tabdel_medium" />
 <param name="include_feature_length_file" value="true"/>
 <param name="ref_source" value="history" />
 <output name="output_medium" file="output_1_medium.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" />
+<param name="anno_select" value="gtf"/>
 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
 <param name="format" value="tabdel_full" />
 <param name="include_feature_length_file" value="true"/>
 <param name="ref_source" value="history" />
 <output name="output_full" file="output_1_full.tab">
 </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" />
+<param name="anno_select" value="gtf"/>
+<param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+<param name="format" value="tabdel_short" />
+<param name="include_feature_length_file" value="true"/>
+<param name="ref_source" value="history" />
+<param name="count_exon_exon_junction_reads" value="-J"/>
+<output name="output_short" file="output_1_short_with_header.tab">
+<metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
+</output>
+<output name="output_summary" file="output_1_summary_with_header.tab">
+<metadata name="column_names" value="Status,featureCounts_input1.bam"/>
+</output>
+<output name="output_jcounts" file="output_1_jcounts_with_header.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 built-in annotation works -->
+<test expect_num_outputs="2">
+<param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" />
+<param name="anno_select" value="builtin"/>
+<param name="format" value="tabdel_short" />
+<param name="genome" value="hg19" />
+<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"/>
+</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 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
-Gene regions should be provided in the GFF/GTF 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 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.
 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 Galaxy wrapper by IUC. Column names are added as metadata object.
+.. _Subread: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
 ]]></help>
 <citations>
 <citation type="doi">10.1093/bioinformatics/btt656</citation>
 </citations>
 </tool>

Mercurial > repos > iuc > featurecounts

comparison featurecounts.xml @ 10:7d1e37c6ef85 draft