Mercurial > repos > lparsons > htseq_count
diff htseq-count.xml @ 3:f7a5b54a8d4f
Split feature and non-feature counts, removed tool_dependencies.xml (for now)
author | Lance Parsons <lparsons@princeton.edu> |
---|---|
date | Mon, 10 Sep 2012 17:30:10 -0400 |
parents | 3fdeebd7e710 |
children | 14bec14f4290 |
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--- a/htseq-count.xml Tue Sep 04 14:16:33 2012 -0400 +++ b/htseq-count.xml Mon Sep 10 17:30:10 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="htseq_count" name="htseq-count" version="0.1"> +<tool id="htseq_count" name="htseq-count" version="0.2"> <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> <requirements> @@ -35,7 +35,7 @@ $samfile #end if $gfffile - > $counts + | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts #if $samout_conditional.samout: && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile #end if</command> @@ -93,6 +93,7 @@ <outputs> <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/> + <data format="tabular" name="othercounts" label="${tool.name} on ${on_string} (no feature)"/> <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)"> <filter>samout_conditional['samout']</filter> </data> @@ -108,12 +109,14 @@ <param name="gfffile" value="htseq-test.gff" /> <param name="samout" value="False" /> <output name="counts" file="htseq-test_counts.tsv" /> + <output name="othercounts" file="htseq-test_othercounts.tsv" /> </test> <test> <param name="samfile" value="htseq-test.bam" /> <param name="gfffile" value="htseq-test.gff" /> <param name="samout" value="False" /> <output name="counts" file="htseq-test_counts.tsv" /> + <output name="othercounts" file="htseq-test_othercounts.tsv" /> </test> <!-- Seems to be an issue setting the $reference_fasta_filename variable during test <test> @@ -123,6 +126,7 @@ <param name="reference_source_selector" value="history" /> <param name="ref_file" value="htseq-test_reference.fasta" /> <output name="counts" file="htseq-test_counts.tsv" /> + <output name="othercounts" file="htseq-test_othercounts.tsv" /> <output name="samoutfile" file="htseq-test_samout.bam" /> </test> -->