Mercurial > repos > lparsons > htseq_count
comparison htseq-count.xml @ 4:359d40333595
Added tool dependencies, updated tests to use small datasets
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Tue, 04 Sep 2012 13:34:05 -0400 |
| parents | c6d73933f601 |
| children | 0a835934d792 |
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| 3:c6d73933f601 | 4:359d40333595 |
|---|---|
| 1 <tool id="htseq_count" name="htseq-count" version="0.1"> | 1 <tool id="htseq_count" name="htseq-count" version="0.1"> |
| 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="1.6.2">numpy</requirement> | 5 <requirement type="package" version="0.5.3p9">htseq</requirement> |
| 6 <requirement type="package" version="0.5.3.p9">htseq</requirement> | |
| 7 <requirement type="package" version="0.1.18">samtools</requirement> | 6 <requirement type="package" version="0.1.18">samtools</requirement> |
| 8 </requirements> | 7 </requirements> |
| 9 <command> | 8 <command> |
| 10 ##set up input files | 9 ##set up input files |
| 11 #set $reference_fasta_filename = "localref.fa" | 10 #set $reference_fasta_filename = "localref.fa" |
| 125 <param name="ref_file" value="htseq-test_reference.fasta" /> | 124 <param name="ref_file" value="htseq-test_reference.fasta" /> |
| 126 <output name="counts" file="htseq-test_counts.tsv" /> | 125 <output name="counts" file="htseq-test_counts.tsv" /> |
| 127 <output name="samoutfile" file="htseq-test_samout.bam" /> | 126 <output name="samoutfile" file="htseq-test_samout.bam" /> |
| 128 </test> | 127 </test> |
| 129 --> | 128 --> |
| 130 | |
| 131 </tests> | 129 </tests> |
| 132 | 130 |
| 133 <help> | 131 <help> |
| 134 Overview | 132 Overview |
| 135 -------- | 133 -------- |
| 222 | 220 |
| 223 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology | 221 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology |
| 224 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General | 222 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General |
| 225 Public License v3. Part of the 'HTSeq' framework. | 223 Public License v3. Part of the 'HTSeq' framework. |
| 226 </help> | 224 </help> |
| 227 | |
| 228 </tool> | 225 </tool> |