Merge pull request #5737 from ARTbio/fix_htseqcount

Upgrade htseq-count tool and fix the "(no feature output)" for compatibility with multiQC tool.
galaxyproject · Jan 31, 2024 · 86a6c88 · 86a6c88
2 parents 0da1ca3 + 263d1e2
commit 86a6c88
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diff --git a/tools/htseq_count/README.rst b/tools/htseq_count/README.rst
@@ -1,7 +1,7 @@
 htseq-count wrapper for Galaxy
 ==============================
 
-Galaxy wrapper for `htseq-count <https://htseq.readthedocs.io/en/release_0.9.1/count.html>`_
+Galaxy wrapper for `htseq-count <https://htseq.readthedocs.io/en/latest/history.html#version-2-0-5>`_
 script from the `HTSEQ <https://readthedocs.org/projects/htseq/>`_ python package.
 
 Installation

diff --git a/tools/htseq_count/htseq-count.xml b/tools/htseq_count/htseq-count.xml
diff --git a/...st-data/htseq-test-paired_othercounts.tsv → ...test-data/htseq-test-paired_allcounts.tsv b/...st-data/htseq-test-paired_othercounts.tsv → ...test-data/htseq-test-paired_allcounts.tsv
@@ -3,3 +3,4 @@ __ambiguous	1
 __too_low_aQual	68
 __not_aligned	0
 __alignment_not_unique	0
+__aligned	317
diff --git a/tools/htseq_count/test-data/htseq-test.gff b/tools/htseq_count/test-data/htseq-test.gff
diff --git a/tools/htseq_count/test-data/htseq-test.gtf b/tools/htseq_count/test-data/htseq-test.gtf
diff --git a/...ount/test-data/htseq-test_othercounts.tsv → ..._count/test-data/htseq-test_allcounts.tsv b/...ount/test-data/htseq-test_othercounts.tsv → ..._count/test-data/htseq-test_allcounts.tsv
@@ -3,3 +3,4 @@ __ambiguous	0
 __too_low_aQual	0
 __not_aligned	1336
 __alignment_not_unique	0
+__aligned	343
diff --git a/tools/htseq_count/test-data/htseq-test_nosq.sam b/tools/htseq_count/test-data/htseq-test_nosq.sam
diff --git a/tools/htseq_count/test-data/htseq-test_samout.bam b/tools/htseq_count/test-data/htseq-test_samout.bam