Repository revision
24:620d5603d1a8

Repository 'htseq_count'
hg clone https://toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count

htseq-count tool metadata
Miscellaneous
htseq-count
- Count aligned reads in a BAM file that overlap features in a GFF file
htseq_count
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3
0.6.1galaxy3
htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3 (this tool)
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy2
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.4.1
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.4
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.3.2
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.3.1
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.3
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.2.1
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.2
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.1
htseq_count
Requirements (dependencies defined in the <requirements> tag set)
name version type
htseq 0.6.1.post1 package
samtools 1.3.1 package
Functional tests
name inputs outputs required files
Test-1 samout_conditional|samout: No
samfile: htseq-test.sam
gfffile: htseq-test.gff
 counts: htseq-test_counts.tsv
othercounts: htseq-test_othercounts.tsv
 htseq-test.sam
htseq-test.gff
htseq-test_counts.tsv
htseq-test_othercounts.tsv
Test-2 samout_conditional|samout: No
force_sort: True
samfile: htseq-test.sam
gfffile: htseq-test.gff
 counts: htseq-test_counts.tsv
othercounts: htseq-test_othercounts.tsv
 htseq-test.sam
htseq-test.gff
htseq-test_counts.tsv
htseq-test_othercounts.tsv
Test-3 samout_conditional|samout: No
samfile: htseq-test.bam
gfffile: htseq-test.gff
 counts: htseq-test_counts.tsv
othercounts: htseq-test_othercounts.tsv
 htseq-test.bam
htseq-test.gff
htseq-test_counts.tsv
htseq-test_othercounts.tsv
Test-4 samout_conditional|samout: No
samfile: htseq-test-paired.bam
gfffile: htseq-test.gff
 counts: htseq-test-paired_counts.tsv
othercounts: htseq-test-paired_othercounts.tsv
 htseq-test-paired.bam
htseq-test.gff
htseq-test-paired_counts.tsv
htseq-test-paired_othercounts.tsv
Test-5 samout_conditional|samout: No
force_sort: True
samfile: htseq-test-paired.bam
gfffile: htseq-test.gff
 counts: htseq-test-paired_counts.tsv
othercounts: htseq-test-paired_othercounts.tsv
 htseq-test-paired.bam
htseq-test.gff
htseq-test-paired_counts.tsv
htseq-test-paired_othercounts.tsv
Test-6 samout_conditional|samout: Yes
samout_conditional|reference_source|ref_file: htseq-test_reference.fasta
samfile: htseq-test.sam
gfffile: htseq-test.gff
samout_conditional|reference_source|reference_source_selector: history
 counts: htseq-test_counts.tsv
othercounts: htseq-test_othercounts.tsv
samoutfile: htseq-test_samout.bam
 htseq-test.sam
htseq-test.gff
htseq-test_reference.fasta
htseq-test_counts.tsv
htseq-test_othercounts.tsv
htseq-test_samout.bam