Mercurial > repos > lparsons > htseq_count

comparison htseq-count.xml @ 28:916cb26bd9d3 draft

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"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
comparison
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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>