Mercurial > repos > iuc > hmmer_hmmsearch

comparison macros.xml @ 6:192a5046d9a2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
author iuc
date Thu, 14 Jan 2021 15:39:33 +0000
parents b774ae8e1609
children d753d9169482
comparison
equal deleted inserted replaced
5:b774ae8e1609 6:192a5046d9a2
224 </when> 224 </when>
225 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)--> 225 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)-->
226 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)--> 226 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)-->
227 </conditional> 227 </conditional>
228 </xml> 228 </xml>
229 <token name="@ADDTHREADS@"><![CDATA[
230 ##compute the number of ADDITIONAL threads to be used (--cpu)
231 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
232 ]]></token>
229 <token name="@CPU@"> 233 <token name="@CPU@">
230 --cpu \${GALAXY_SLOTS:-2} 234 --cpu \$addthreads
231 </token> 235 </token>
232 <token name="@SEED@"> 236 <token name="@SEED@">
233 --seed $seed 237 --seed $seed
234 </token> 238 </token>
235 <xml name="seed"> 239 <xml name="seed">
560 564
561 565
562 **Advanced Documentation** 566 **Advanced Documentation**
563 567
564 A more detailed look at the internals of the various filter pipelines was 568 A more detailed look at the internals of the various filter pipelines was
565 posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__. 569 posted on the `developer's blog <http://cryptogenomicon.org/hmmer3-is-stubborn.html>`__.
566 The information posted there may be useful to those who are struggling with 570 The information posted there may be useful to those who are struggling with
567 poor-scoring sequences. 571 poor-scoring sequences.
568
569 ]]></token> 572 ]]></token>
570 <token name="@ADV_OPTS_HELP@"><![CDATA[ 573 <token name="@ADV_OPTS_HELP@"><![CDATA[
571 Advanced Options 574 Advanced Options
572 ---------------- 575 ----------------
573 576