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comparison codeml.xml @ 4:f9cb3a4339c2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
author iuc
date Sat, 27 Nov 2021 09:55:34 +0000
parents b2b8e75a962d
children dba114391c98
comparison
equal deleted inserted replaced
3:b2b8e75a962d 4:f9cb3a4339c2
1 <tool name="codeML" id="codeml" version="@WRAPPER_VERSION@+galaxy1" profile="18.01"> 1 <tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy2" profile="18.01">
2 <description> 2 <description>
3 Detects positive selection (paml package) 3 Detects positive selection (paml package)
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 9
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@WRAPPER_VERSION@">paml</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">paml</requirement>
12 </requirements> 12 </requirements>
13 13
14 <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command> 14 <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
54 alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate) 54 alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate)
55 Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha 55 Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha
56 ncatG = $adv.ncatG * # of categories in dG of NSsites models 56 ncatG = $adv.ncatG * # of categories in dG of NSsites models
57 fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho 57 fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho
58 rho = $adv.rho * initial or fixed rho, 0:no correlation 58 rho = $adv.rho * initial or fixed rho, 0:no correlation
59 getSE = $adv.getSE * 0: don't want them, 1: want S.E.s of estimates 59 getSE = $adv.getSE * 0: dont want them, 1: want S.E.s of estimates
60 RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) 60 RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
61 Small_Diff = $adv.Small_Diff 61 Small_Diff = $adv.Small_Diff
62 cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)? 62 cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)?
63 fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed 63 fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed
64 method = $adv.method * 0: simultaneous; 1: one branch at a time 64 method = $adv.method * 0: simultaneous; 1: one branch at a time
236 </section> 236 </section>
237 </inputs> 237 </inputs>
238 238
239 <outputs> 239 <outputs>
240 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" /> 240 <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
241 <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" > 241 <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
242 <filter>adv['seqtype']=="1"</filter> 242 <filter>adv['seqtype']=="1"</filter>
243 </data> 243 </data>
244 <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" > 244 <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
245 <filter>adv['seqtype']=="1"</filter> 245 <filter>adv['seqtype']=="1"</filter>
246 </data> 246 </data>
247 <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" > 247 <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
248 <filter>adv['seqtype']=="1"</filter> 248 <filter>adv['seqtype']=="1"</filter>
249 </data> 249 </data>
250 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/> 250 <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
251 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/> 251 <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
252 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/> 252 <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
253 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/> 253 <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
254 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/> 254 <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
255 <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc"> 255 <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
256 <filter>adv['verbose']=="1"</filter> 256 <filter>adv['verbose']=="1"</filter>
257 </data> 257 </data>
258 </outputs> 258 </outputs>
259 259
260 <tests> 260 <tests>
261 <test> 261 <test expect_num_outputs="9">
262 <conditional name="compat_model" > 262 <conditional name="compat_model" >
263 <param name="brmodel" value="0" /> 263 <param name="brmodel" value="0" />
264 <param name="NSsites" value="0" /> 264 <param name="NSsites" value="0" />
265 </conditional> 265 </conditional>
266 <param name="adv.fix_omega" value="0" /> 266 <param name="adv|fix_omega" value="0" />
267 <param name="adv.omega" value="0.2" /> 267 <param name="adv|omega" value="0.2" />
268 <param name="RateAncestor" value="1" /> 268 <param name="RateAncestor" value="1" />
269 <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> 269 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
270 <param name="tree" ftype="txt" value="RAxML_bestTree" /> 270 <param name="tree" value="RAxML_bestTree" ftype="nhx" />
271 <output name="2ngdn" value="1_2ngdn" /> 271 <output name="twongdn" value="1_2ngdn" />
272 <output name="2ngds" value="1_2ngds" /> 272 <output name="twongds" value="1_2ngds" />
273 <output name="2ngt" value="1_2ngt" /> 273 <output name="twongt" value="1_2ngt" />
274 <output name="run"> 274 <output name="run">
275 <assert_contents> 275 <assert_contents>
276 <has_text text="CODONML (in paml version 4.9, March 2015)"/> 276 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
277 <has_text text="Time used:" /> 277 <has_text text="Time used:" />
278 </assert_contents> 278 </assert_contents>
279 </output> 279 </output>
280 <output name="ctl" value="1_codeml.ctl" lines_diff="4" /> 280 <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
281 </test> 281 </test>
282 <test> 282 <test expect_num_outputs="9">
283 <conditional name="compat_model" > 283 <conditional name="compat_model" >
284 <param name="brmodel" value="2" /> 284 <param name="brmodel" value="2" />
285 <param name="NSsites" value="0" /> 285 <param name="NSsites" value="0" />
286 </conditional> 286 </conditional>
287 <param name="adv.fix_omega" value="0" /> 287 <param name="adv|fix_omega" value="0" />
288 <param name="adv.omega" value="0.2" /> 288 <param name="adv|omega" value="0.2" />
289 <param name="RateAncestor" value="1" /> 289 <param name="RateAncestor" value="1" />
290 <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> 290 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
291 <param name="tree" ftype="txt" value="tree_model2" /> 291 <param name="tree" value="tree_model2" ftype="nhx" />
292 <output name="2ngdn" value="2_2ngdn" /> 292 <output name="twongdn" value="2_2ngdn" />
293 <output name="2ngds" value="2_2ngds" /> 293 <output name="twongds" value="2_2ngds" />
294 <output name="2ngt" value="2_2ngt" /> 294 <output name="twongt" value="2_2ngt" />
295 <output name="run"> 295 <output name="run">
296 <assert_contents> 296 <assert_contents>
297 <has_text text="CODONML (in paml version 4.9, March 2015)"/> 297 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
298 <has_text text="Time used:" /> 298 <has_text text="Time used:" />
299 </assert_contents> 299 </assert_contents>
300 </output> 300 </output>
301 <output name="ctl" value="2_codeml.ctl" lines_diff="4" /> 301 <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
302 </test> 302 </test>
303 <test> 303 <test expect_num_outputs="9">
304 <conditional name="compat_model" > 304 <conditional name="compat_model" >
305 <param name="brmodel" value="3" /> 305 <param name="brmodel" value="3" />
306 <param name="NSsites" value="2" /> 306 <param name="NSsites" value="2" />
307 </conditional> 307 </conditional>
308 <param name="adv.fix_omega" value="0" /> 308 <param name="adv|fix_omega" value="0" />
309 <param name="adv.omega" value="0.2" /> 309 <param name="adv|omega" value="0.2" />
310 <param name="RateAncestor" value="1" /> 310 <param name="RateAncestor" value="1" />
311 <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> 311 <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
312 <param name="tree" ftype="txt" value="tree_model3" /> 312 <param name="tree" value="tree_model3" ftype="nhx" />
313 <output name="2ngdn" value="3_2ngdn" /> 313 <output name="twongdn" value="3_2ngdn" />
314 <output name="2ngds" value="3_2ngds" /> 314 <output name="twongds" value="3_2ngds" />
315 <output name="2ngt" value="3_2ngt" /> 315 <output name="twongt" value="3_2ngt" />
316 <output name="run"> 316 <output name="run">
317 <assert_contents> 317 <assert_contents>
318 <has_text text="CODONML (in paml version 4.9, March 2015)"/> 318 <has_text text="CODONML (in paml version 4.9, March 2015)"/>
319 <has_text text="Time used:" /> 319 <has_text text="Time used:" />
320 </assert_contents> 320 </assert_contents>