Mercurial > repos > lparsons > htseq_count
changeset 24:620d5603d1a8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
| author | iuc |
|---|---|
| date | Fri, 20 Jan 2017 15:46:13 -0500 |
| parents | 6e5c95760ab1 |
| children | f1368427a79c |
| files | htseq-count.xml test-data/htseq-test_samout.bam |
| diffstat | 2 files changed, 14 insertions(+), 16 deletions(-) [+] |
line wrap: on
line diff
--- a/htseq-count.xml Wed Sep 21 10:59:41 2016 -0400 +++ b/htseq-count.xml Fri Jan 20 15:46:13 2017 -0500 @@ -1,8 +1,8 @@ -<tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2"> +<tool id="htseq_count" name="htseq-count" version="0.6.1galaxy3" profile="16.04"> <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> <requirements> <requirement type="package" version="0.6.1.post1">htseq</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> </requirements> <stdio> @@ -23,26 +23,26 @@ #if $samout_conditional.samout == "Yes": #if str( $samout_conditional.reference_source.reference_source_selector ) == "history": ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" && - samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 && + samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 && #else: #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) #end if #end if - + #if $force_sort == "True": #if $samfile.extension == 'bam': - samtools sort -n "$samfile" "name_sorted_alignment" && + samtools sort -n -o 'name_sorted_alignment.bam' '$samfile' && #else - samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" | samtools sort -n - "name_sorted_alignment" && + samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -o 'name_sorted_alignment.bam' - && #end if #end if - + htseq-count --mode=$mode --stranded=$stranded --minaqual=$minaqual - --type="$featuretype" - --idattr="$idattr" + --type='$featuretype' + --idattr='$idattr' #if $samout_conditional.samout == "Yes": --samout='$__new_file_path__/${samoutfile.id}_tmp' #end if @@ -55,16 +55,16 @@ --format=$samfile.extension '$samfile' #end if - + "$gfffile" | 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 $samout_conditional.samout == "Yes": && samtools view -Su - -t "${reference_fasta_filename}.fai" - "$__new_file_path__/${samoutfile.id}_tmp" - | samtools sort -o - name_sorted_alignment > "$samoutfile" + -t '${reference_fasta_filename}.fai' + '$__new_file_path__/${samoutfile.id}_tmp' + | samtools sort -o '$samoutfile' - #end if ]]> </command> @@ -179,7 +179,6 @@ <output name="counts" file="htseq-test-paired_counts.tsv" /> <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> </test> - <test> <param name="samfile" value="htseq-test.sam" /> <param name="gfffile" value="htseq-test.gff" /> @@ -285,7 +284,6 @@ Public License v3. Part of the 'HTSeq' framework. ]]> </help> - <citations> <citation type="doi">10.1093/bioinformatics/btu638</citation> </citations>