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comparison macros.xml @ 13:0e60e2dd20af draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:25:11 +0000
parents 9bd1568619cd
children
comparison
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12:9bd1568619cd 13:0e60e2dd20af
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 <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
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>