comparison macros.xml @ 6:6846f8789e33 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"

5:750269125dc9

      </when>
      <!-- -mx <s>      : substitution score matrix (built-in matrices, with -singlemx)-->
      <!-- -mxfile <f>  : read substitution score matrix from file <f> (with -singlemx)-->
    </conditional>
  </xml>
  <token name="@CPU@">
      --cpu \${GALAXY_SLOTS:-2}
  </token>
  <token name="@SEED@">
      --seed $seed
  </token>
  <xml name="seed">

**Advanced Documentation**

A more detailed look at the internals of the various filter pipelines was
posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__.
The information posted there may be useful to those who are struggling with
poor-scoring sequences.

]]></token>
  <token name="@ADV_OPTS_HELP@"><![CDATA[
Advanced Options
----------------

6:6846f8789e33

      </when>
      <!-- -mx <s>      : substitution score matrix (built-in matrices, with -singlemx)-->
      <!-- -mxfile <f>  : read substitution score matrix from file <f> (with -singlemx)-->
    </conditional>
  </xml>
  <token name="@ADDTHREADS@"><![CDATA[
        ##compute the number of ADDITIONAL threads to be used (--cpu)
        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
    ]]></token>
  <token name="@CPU@">
      --cpu \$addthreads
  </token>
  <token name="@SEED@">
      --seed $seed
  </token>
  <xml name="seed">

**Advanced Documentation**

A more detailed look at the internals of the various filter pipelines was
posted on the `developer's blog <http://cryptogenomicon.org/hmmer3-is-stubborn.html>`__.
The information posted there may be useful to those who are struggling with
poor-scoring sequences.
]]></token>
  <token name="@ADV_OPTS_HELP@"><![CDATA[
Advanced Options
----------------