Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.xml @ 10:59bb87024183 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 15 Jan 2016 08:44:00 -0500
parents 338e991cdd1f
children 9886ad53474a
comparison
equal deleted inserted replaced
9:8cc00c5cf33e 10:59bb87024183
1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.0"> 1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.0">
2 <description>using coordinates from assembled/unassembled genomes</description> 2 <description>using coordinates from assembled/unassembled genomes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.1">bx-python</requirement>
4 <requirement type="package" version="35x1">faToTwoBit</requirement> 5 <requirement type="package" version="35x1">faToTwoBit</requirement>
5 </requirements> 6 </requirements>
6 <command> 7 <command>
7 <![CDATA[ 8 <![CDATA[
8 #set genome = $input.metadata.dbkey 9 #set genome = $input.metadata.dbkey
28 --output_format $output_format 29 --output_format $output_format
29 --output $output 30 --output $output
30 ]]> 31 ]]>
31 </command> 32 </command>
32 <inputs> 33 <inputs>
33 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in" help="Supported formats are gff, interval"> 34 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in">
34 <validator type="unspecified_build" /> 35 <validator type="unspecified_build" />
35 </param> 36 </param>
36 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is gff"> 37 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is in the gff family">
37 <option value="yes">Yes</option> 38 <option value="yes">Yes</option>
38 <option value="no">No</option> 39 <option value="no">No</option>
39 </param> 40 </param>
40 <conditional name="reference_genome_cond"> 41 <conditional name="reference_genome_cond">
41 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome"> 42 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
189 190
190 </help> 191 </help>
191 <citations> 192 <citations>
192 <citation type="bibtex"> 193 <citation type="bibtex">
193 @unpublished{None, 194 @unpublished{None,
194 author = {}, 195 author = {Guru Ananda,Greg Von Kuster},
195 title = {None}, 196 title = {None},
196 year = {None}, 197 year = {None},
197 eprint = {None}, 198 eprint = {None},
198 url = {http://www.bx.psu.edu/~anton/labSite/} 199 url = {http://www.bx.psu.edu/~anton/labSite/}
199 }</citation> 200 }</citation>