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comparison htseq-count.xml @ 17:d5edaf8dc974 draft

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Fixed test output, added missing pysam dependency
author lparsons
date Fri, 11 Apr 2014 16:01:54 -0400
parents 227f9d3f0e32
children 3b3601a2a7c7
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16:227f9d3f0e32 17:d5edaf8dc974
1 <tool id="htseq_count" name="htseq-count" version="0.4"> 1 <tool id="htseq_count" name="htseq-count" version="0.4.1">
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 <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> 3 <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.7.1">numpy</requirement> 5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="0.6.1">htseq</requirement> 6 <requirement type="package" version="0.6.1">htseq</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement> 7 <requirement type="package" version="0.1.19">samtools</requirement>
8 <requirement type="package" version="0.7.7">pysam</requirement>
8 </requirements> 9 </requirements>
9 <command> 10 <command>
10 ##set up input files 11 ##set up input files
11 #set $reference_fasta_filename = "localref.fa" 12 #set $reference_fasta_filename = "localref.fa"
12 #if $samout_conditional.samout: 13 #if $samout_conditional.samout: