Mercurial > repos > iuc > hmmer_jackhmmer

comparison macros.xml @ 9:9fdeca68a6b5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee
author iuc
date Sun, 25 Feb 2024 18:32:59 +0000
parents 5cbef50c0c63
children
comparison
equal deleted inserted replaced
8:5cbef50c0c63 9:9fdeca68a6b5
9 <xml name="bio_tools"> 9 <xml name="bio_tools">
10 <xrefs> 10 <xrefs>
11 <xref type="bio.tools">hmmer3</xref> 11 <xref type="bio.tools">hmmer3</xref>
12 </xrefs> 12 </xrefs>
13 </xml> 13 </xml>
14 <token name="@TOOL_VERSION@">3.3.2</token> 14 <token name="@TOOL_VERSION@">3.4</token>
15 <xml name="stdio"> 15 <token name="@PROFILE@">22.05</token>
16 <stdio>
17 <!-- Anything other than zero is an error -->
18 <exit_code range="1:"/>
19 <exit_code range=":-1"/>
20 <!-- In case the return code has not been set propery check stderr too -->
21 <regex match="Error:"/>
22 <regex match="Exception:"/>
23 </stdio>
24 </xml>
25
26 <!-- command line for thresholds_* --> 16 <!-- command line for thresholds_* -->
27 <token name="@THRESHOLDS@"> 17 <token name="@THRESHOLDS@">
28 #if $repopt.repopt_sel == "evalue" 18 #if $repopt.repopt_sel == "evalue"
29 -E $repopt.E 19 -E $repopt.E
30 #if str($repopt.incE) != "" 20 #if str($repopt.incE) != ""
361 <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option> 351 <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
362 <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option> 352 <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
363 <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option> 353 <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
364 <option value="--wgiven">use weights as given in MSA file (--wgiven)</option> 354 <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
365 </param> 355 </param>
366 <when value="--wpb"> 356 <when value="--wpb"/>
367 </when> 357 <when value="--wgsc"/>
368 <when value="--wgsc">
369 </when>
370 <when value="--wblosum"> 358 <when value="--wblosum">
371 <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" /> 359 <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" />
372 </when> 360 </when>
373 <when value="--wnone"> 361 <when value="--wnone"/>
374 </when> 362 <when value="--wgiven"/>
375 <when value="--wgiven">
376 </when>
377 </conditional> 363 </conditional>
378 </xml> 364 </xml>
379 <token name="@AEEWS@"> 365 <token name="@AEEWS@">
380 #if $aeews.aeews_select != "": 366 #if $aeews.aeews_select != "":
381 --$aeews.aeews_select 367 --$aeews.aeews_select