Mercurial > repos > lparsons > htseq_count
comparison htseq-count.xml @ 28:916cb26bd9d3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 9b894593cf3c0156faf679300ded731e0796f792"
| author | iuc |
|---|---|
| date | Sun, 26 Jan 2020 23:43:52 -0500 |
| parents | 67b0b160903a |
| children | 4418229c501e |
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| 27:67b0b160903a | 28:916cb26bd9d3 |
|---|---|
| 1 <tool id="htseq_count" name="htseq-count" version="0.9.1" profile="16.04"> | 1 <tool id="htseq_count" name="htseq-count" version="0.9.1+galaxy1" profile="16.04"> |
| 2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> | 2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.9.1">htseq</requirement> | 4 <requirement type="package" version="0.9.1">htseq</requirement> |
| 5 <requirement type="package" version="1.7">samtools</requirement> | 5 <requirement type="package" version="1.7">samtools</requirement> |
| 6 </requirements> | 6 </requirements> |
| 47 #if str( $advanced_options.advanced_options_selector ) == "advanced": | 47 #if str( $advanced_options.advanced_options_selector ) == "advanced": |
| 48 --nonunique=$advanced_options.nonunique | 48 --nonunique=$advanced_options.nonunique |
| 49 --secondary-alignments=${advanced_options.secondary_alignments} | 49 --secondary-alignments=${advanced_options.secondary_alignments} |
| 50 --supplementary-alignments=${advanced_options.supplementary_alignments} | 50 --supplementary-alignments=${advanced_options.supplementary_alignments} |
| 51 #if $advanced_options.samout_conditional.samout == "Yes": | 51 #if $advanced_options.samout_conditional.samout == "Yes": |
| 52 --samout='$__new_file_path__/${samoutfile.id}_tmp.sam' | 52 --samout=samout.sam |
| 53 #end if | 53 #end if |
| 54 #end if | 54 #end if |
| 55 | 55 |
| 56 --order=name | 56 --order=name |
| 57 --format=sam | 57 --format=sam |
| 63 | 63 |
| 64 #if str( $advanced_options.advanced_options_selector ) == "advanced": | 64 #if str( $advanced_options.advanced_options_selector ) == "advanced": |
| 65 #if $advanced_options.samout_conditional.samout == "Yes": | 65 #if $advanced_options.samout_conditional.samout == "Yes": |
| 66 && samtools view -Su | 66 && samtools view -Su |
| 67 -t '${reference_fasta_filename}.fai' | 67 -t '${reference_fasta_filename}.fai' |
| 68 '$__new_file_path__/${samoutfile.id}_tmp.sam' | 68 samout.sam |
| 69 | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' - | 69 | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' - |
| 70 #end if | 70 #end if |
| 71 #end if | 71 #end if |
| 72 ]]> | 72 ]]> |
| 73 </command> | 73 </command> |