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comparison macros.xml @ 4:971dc85e9441 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:14:44 +0000
parents 56faa6a57e50
children
comparison
equal deleted inserted replaced
3:56faa6a57e50 4:971dc85e9441
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 <!-- NOTE: for some tools only the version of the requirement but not the
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` -->
8 <token name="@TOOL_VERSION@">1.15.1</token> 14 <token name="@TOOL_VERSION@">1.15.1</token>
15 <token name="@VERSION_SUFFIX@">2</token>
9 <token name="@PROFILE@">20.05</token> 16 <token name="@PROFILE@">20.05</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(',')))
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>