Mercurial > repos > devteam > samtools_split

comparison macros.xml @ 7:b6caca6a4ca5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:23:35 +0000
parents eda9f7aa1d54
children
comparison
equal deleted inserted replaced
6:eda9f7aa1d54 7:b6caca6a4ca5
3 <requirements> 3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> 4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@TOOL_VERSION@">1.15.1</token> 8 <!-- NOTE: for some tools only the version of the requirement but not the
9 <token name="@PROFILE@">20.05</token> 9 tool's version is controlled by the TOOL_VERSION token
10 (because their version is ahead of the requirement version ..
11 please only bump the minor version in order to let the requirement
12 version catch up eventually). To find the tools check:
13 `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
14 <token name="@TOOL_VERSION@">1.20</token>
15 <token name="@VERSION_SUFFIX@">2</token>
16 <token name="@PROFILE@">22.05</token>
10 <token name="@FLAGS@"><![CDATA[ 17 <token name="@FLAGS@"><![CDATA[
11 #set $flags = 0 18 #set $flags = 0
12 #if $filter 19 #if $filter
13 #set $flags = sum(map(int, str($filter).split(','))) 20 #set $flags = sum(map(int, str($filter).split(',')))
14 #end if 21 #end if
210 </conditional> 217 </conditional>
211 </xml> 218 </xml>
212 219
213 <xml name="citations"> 220 <xml name="citations">
214 <citations> 221 <citations>
215 <citation type="bibtex"> 222 <citation type="doi">10.1093/gigascience/giab008</citation>
216 @misc{SAM_def,
217 title={Definition of SAM/BAM format},
218 url = {https://samtools.github.io/hts-specs/},}
219 </citation>
220 <citation type="doi">10.1093/bioinformatics/btp352</citation>
221 <citation type="doi">10.1093/bioinformatics/btr076</citation>
222 <citation type="doi">10.1093/bioinformatics/btr509</citation>
223 <citation type="bibtex">
224 @misc{Danecek_et_al,
225 Author={Danecek, P., Schiffels, S., Durbin, R.},
226 title={Multiallelic calling model in bcftools (-m)},
227 url = {http://samtools.github.io/bcftools/call-m.pdf},}
228 </citation>
229 <citation type="bibtex">
230 @misc{Durbin_VCQC,
231 Author={Durbin, R.},
232 title={Segregation based metric for variant call QC},
233 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
234 </citation>
235 <citation type="bibtex">
236 @misc{Li_SamMath,
237 Author={Li, H.},
238 title={Mathematical Notes on SAMtools Algorithms},
239 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
240 </citation>
241 <citation type="bibtex">
242 @misc{SamTools_github,
243 title={SAMTools GitHub page},
244 url = {https://github.com/samtools/samtools},}
245 </citation>
246 </citations> 223 </citations>
247 </xml> 224 </xml>
248 <xml name="version_command"> 225 <xml name="version_command">
249 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> 226 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
250 </xml> 227 </xml>