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comparison macros.xml @ 7:c89806670ab9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:14:35 +0000
parents 92ec40abcdcf
children 26b4f9f98aca
comparison
equal deleted inserted replaced
6:92ec40abcdcf 7:c89806670ab9
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@">1.13</token> 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` -->
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(',')))
101 #else 108 #else
102 #set use_ref=False 109 #set use_ref=False
103 #end if 110 #end if
104 ]]></token> 111 ]]></token>
105 112
106 <xml name="optional_reference"> 113 <xml name="optional_reference" token_help="" token_argument="">
107 <conditional name="addref_cond"> 114 <conditional name="addref_cond">
108 <param name="addref_select" type="select" label="Use a reference sequence"> 115 <param name="addref_select" type="select" label="Use a reference sequence">
109 <help>@HELP@</help> 116 <help>@HELP@</help>
110 <option value="no">No</option> 117 <option value="no">No</option>
111 <option value="history">Use a genome/index from the history</option> 118 <option value="history">Use a genome/index from the history</option>
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>