| Previous changeset 31:6f66ae7c5f7a (2023-03-02) Next changeset 33:1b851f87fbe0 (2024-10-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1 |
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modified:
featurecounts.xml |
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added:
test-data/subset.sorted.featurecounts_short.tab test-data/subset.sorted.featurecounts_summary.tab |
| b |
| diff -r 6f66ae7c5f7a -r f9d49f5cb597 featurecounts.xml --- a/featurecounts.xml Thu Mar 02 12:50:54 2023 +0000 +++ b/featurecounts.xml Sat Sep 09 21:18:37 2023 +0000 |
| b |
| @@ -2,7 +2,7 @@ <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> <macros> <token name="@TOOL_VERSION@">2.0.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <macro name="conditional_gff_opions"> <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."/> @@ -137,7 +137,7 @@ <param name="alignment" type="data" multiple="false" - format="bam,sam" + format="unsorted.bam,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> @@ -487,7 +487,7 @@ </outputs> <tests> <test expect_num_outputs="3"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.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"/> @@ -500,7 +500,7 @@ </output> </test> <test expect_num_outputs="3"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.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"/> @@ -516,7 +516,7 @@ </output> </test> <test expect_num_outputs="4"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.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"/> @@ -534,7 +534,7 @@ </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="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/> <param name="anno_select" value="builtin"/> <param name="format" value="tabdel_short"/> <conditional name="pe_parameters"> @@ -551,7 +551,7 @@ </test> <!-- Ensure fragment counting works --> <test expect_num_outputs="3"> - <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/> + <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/> <param name="anno_select" value="builtin"/> <param name="format" value="tabdel_short"/> <conditional name="pe_parameters"> @@ -568,7 +568,7 @@ </test> <!-- Ensure cached GTFs work --> <test expect_num_outputs="3"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/> <param name="anno_select" value="cached"/> <param name="format" value="tabdel_medium"/> <param name="include_feature_length_file" value="true"/> @@ -580,7 +580,7 @@ </output> </test> <!-- Ensure BAM output works --> - <test> + <test expect_num_outputs="3"> <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"/> @@ -588,6 +588,10 @@ <param name="R" value="true"/> </section> <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/> + <output name="output_short" file="subset.sorted.featurecounts_short.tab"> + <metadata name="column_names" value="Geneid,subset.sorted.bam"/> + </output> + <output name="output_summary" file="subset.sorted.featurecounts_summary.tab"/> </test> </tests> |
| b |
| diff -r 6f66ae7c5f7a -r f9d49f5cb597 test-data/subset.sorted.featurecounts_short.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset.sorted.featurecounts_short.tab Sat Sep 09 21:18:37 2023 +0000 |
| b |
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|
| b |
| diff -r 6f66ae7c5f7a -r f9d49f5cb597 test-data/subset.sorted.featurecounts_summary.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset.sorted.featurecounts_summary.tab Sat Sep 09 21:18:37 2023 +0000 |
| b |
| @@ -0,0 +1,15 @@ +Status subset.sorted.bam +Assigned 14 +Unassigned_Unmapped 0 +Unassigned_Read_Type 0 +Unassigned_Singleton 0 +Unassigned_MappingQuality 0 +Unassigned_Chimera 0 +Unassigned_FragmentLength 0 +Unassigned_Duplicate 0 +Unassigned_MultiMapping 3840 +Unassigned_Secondary 0 +Unassigned_NonSplit 0 +Unassigned_NoFeatures 5082 +Unassigned_Overlapping_Length 0 +Unassigned_Ambiguity 0 |