| Previous changeset 9:e6a2a912677a (2017-11-17) Next changeset 11:e803ca6407c0 (2018-03-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8 |
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modified:
featurecounts.xml |
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added:
test-data/output_1_jcounts_with_header.tab test-data/output_1_short_with_header.tab test-data/output_1_summary_with_header.tab test-data/output_builtin_hg19.tab test-data/output_summary_builtin_hg19.tab test-data/pairend_strandspecific_51mer_hg19_chr1_1-100000.bam |
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| diff -r e6a2a912677a -r 46cccc52be5f featurecounts.xml --- a/featurecounts.xml Fri Nov 17 06:02:56 2017 -0500 +++ b/featurecounts.xml Sun Jan 14 09:23:49 2018 -0500 |
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| b'@@ -1,17 +1,27 @@\n-<tool id="featurecounts" name="featureCounts" version="1.6.0.1" profile="16.04">\n+<tool id="featurecounts" name="featureCounts" version="1.6.0.2" profile="16.04">\n <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>\n <requirements>\n <requirement type="package" version="1.6.0">subread</requirement>\n </requirements>\n \n <version_command>featureCounts -v 2>&1 | grep .</version_command>\n- <command><![CDATA[\n+ <command detect_errors="exit_code"><![CDATA[\n+ ## Export fc path for its built-in annotation\n+ export FC_PATH=\\$(command -v featureCounts | sed \'s@/bin/featureCounts$@@\') &&\n+\n ## Check whether all alignments are from the same type (bam || sam)\n featureCounts\n- #if $gtf_source.ref_source=="history":\n- -a \'$gtf_source.reference_gene_sets\'\n- #else:\n- -a \'$gtf_source.reference_gene_sets_builtin.fields.path\'\n+\n+ #if $anno.anno_select=="gtf":\n+ #if $anno.gtf_source.ref_source=="history":\n+ -a \'$anno.gtf_source.reference_gene_sets\'\n+ #else:\n+ -a \'$anno.gtf_source.reference_gene_sets_builtin.fields.path\'\n+ #end if\n+ -F "GTF"\n+ #elif $anno.anno_select=="builtin":\n+ -a \\${FC_PATH}/annotation/${anno.genome}_RefSeq_exon.txt\n+ -F "SAF"\n #end if\n \n -o "output"\n@@ -24,13 +34,13 @@\n -s $extended_parameters.strand_specificity\n $extended_parameters.multimapping_enabled.multimapping_counts\n \n- #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M"\n+ #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":\n $extended_parameters.multimapping_enabled.fraction\n #end if\n \n $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads\n- #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"\n- #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome\n+ #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":\n+ #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:\n -G \'$extended_parameters.exon_exon_junction_read_counting_enabled.genome\'\n #end if\n #end if\n@@ -48,18 +58,18 @@\n $extended_parameters.primary\n $extended_parameters.ignore_dup\n \n- #if str($extended_parameters.read_extension_5p) != "0"\n+ #if str($extended_parameters.read_extension_5p) != "0":\n --readExtension5 $extended_parameters.read_extension_5p\n #end if\n \n- #if str($extended_parameters.read_extension_3p) != "0"\n+ #if str($extended_parameters.read_extension_3p) != "0":\n --readExtension3 $extended_parameters.read_extension_3p\n #end if\n \n $pe_parameters.fragment_counting_enabled.fragment_counting\n- #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p"\n+ #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p":\n $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance\n- #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P"\n+ #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P":\n -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_'..b'" />\n <param name="format" value="tabdel_full" />\n <param name="include_feature_length_file" value="true"/>\n@@ -479,7 +523,35 @@\n <metadata name="column_names" value="Feature,Length"/>\n </output>\n </test>\n-\n+ <test expect_num_outputs="4">\n+ <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />\n+ <param name="anno_select" value="gtf"/>\n+ <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />\n+ <param name="format" value="tabdel_short" />\n+ <param name="include_feature_length_file" value="true"/>\n+ <param name="ref_source" value="history" />\n+ <param name="count_exon_exon_junction_reads" value="-J"/>\n+ <output name="output_short" file="output_1_short_with_header.tab">\n+ <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>\n+ </output>\n+ <output name="output_summary" file="output_1_summary_with_header.tab">\n+ <metadata name="column_names" value="Status,featureCounts_input1.bam"/>\n+ </output>\n+ <output name="output_jcounts" file="output_1_jcounts_with_header.tab">\n+ <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>\n+ </output>\n+ </test>\n+ <!-- Ensure built-in annotation works -->\n+ <test expect_num_outputs="2">\n+ <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" />\n+ <param name="anno_select" value="builtin"/>\n+ <param name="format" value="tabdel_short" />\n+ <param name="genome" value="hg19" />\n+ <output name="output_short" file="output_builtin_hg19.tab">\n+ <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>\n+ </output>\n+ <output name="output_summary" file="output_summary_builtin_hg19.tab"/>\n+ </test>\n </tests>\n \n <help><![CDATA[\n@@ -488,7 +560,7 @@\n \n Overview\n --------\n-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.\n+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.\n \n Input formats\n -------------\n@@ -497,14 +569,18 @@\n - SAM format, http://samtools.sourceforge.net/samtools.shtml#5\n - BAM format\n \n-Gene regions should be provided in the GFF/GTF format:\n+Annotations for gene regions should be provided in the GFF/GTF format:\n \n - http://genome.ucsc.edu/FAQ/FAQformat.html#format3\n - http://www.ensembl.org/info/website/upload/gff.html\n \n+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.\n+\n Output format\n -------------\n 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.\n+\n+.. _Subread: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf\n ]]></help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/btt656</citation>\n' |
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| diff -r e6a2a912677a -r 46cccc52be5f test-data/output_1_jcounts_with_header.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_1_jcounts_with_header.tab Sun Jan 14 09:23:49 2018 -0500 |
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| @@ -0,0 +1,1 @@ +PrimaryGene SecondaryGenes Site1_chr Site1_location Site1_strand Site2_chr Site2_location Site2_strand featureCounts_input1.bam \ No newline at end of file |
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| diff -r e6a2a912677a -r 46cccc52be5f test-data/output_1_short_with_header.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_1_short_with_header.tab Sun Jan 14 09:23:49 2018 -0500 |
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| @@ -0,0 +1,3 @@ +Geneid featureCounts_input1.bam +left 92 +right 66 |
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| diff -r e6a2a912677a -r 46cccc52be5f test-data/output_1_summary_with_header.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_1_summary_with_header.tab Sun Jan 14 09:23:49 2018 -0500 |
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| @@ -0,0 +1,13 @@ +Status featureCounts_input1.bam +Assigned 158 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_Chimera 0 +Unassigned_FragmentLength 0 +Unassigned_Duplicate 0 +Unassigned_MultiMapping 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_NoFeatures 6078 +Unassigned_Overlapping_Length 0 +Unassigned_Ambiguity 0 |
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| diff -r e6a2a912677a -r 46cccc52be5f test-data/output_builtin_hg19.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_builtin_hg19.tab Sun Jan 14 09:23:49 2018 -0500 |
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|
| b |
| diff -r e6a2a912677a -r 46cccc52be5f test-data/output_summary_builtin_hg19.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary_builtin_hg19.tab Sun Jan 14 09:23:49 2018 -0500 |
| b |
| @@ -0,0 +1,13 @@ +Status pairend_strandspecific_51mer_hg19_chr1_1-100000.bam +Assigned 3 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_Chimera 0 +Unassigned_FragmentLength 0 +Unassigned_Duplicate 0 +Unassigned_MultiMapping 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_NoFeatures 37 +Unassigned_Overlapping_Length 0 +Unassigned_Ambiguity 0 |
| b |
| diff -r e6a2a912677a -r 46cccc52be5f test-data/pairend_strandspecific_51mer_hg19_chr1_1-100000.bam |
| b |
| Binary file test-data/pairend_strandspecific_51mer_hg19_chr1_1-100000.bam has changed |