Mercurial > repos > iuc > hmmer_nhmmer
changeset 6:314b778b8ffa draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
| author | iuc |
|---|---|
| date | Thu, 14 Jan 2021 15:42:52 +0000 |
| parents | b4fe2f703b4b |
| children | b28e8ed99424 |
| files | macros.xml nhmmer.xml |
| diffstat | 2 files changed, 8 insertions(+), 4 deletions(-) [+] |
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--- a/macros.xml Tue Jun 16 05:38:43 2020 -0400 +++ b/macros.xml Thu Jan 14 15:42:52 2021 +0000 @@ -226,8 +226,12 @@ <!-- -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 \${GALAXY_SLOTS:-2} + --cpu \$addthreads </token> <token name="@SEED@"> --seed $seed @@ -562,10 +566,9 @@ **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/>`__. +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
--- a/nhmmer.xml Tue Jun 16 05:38:43 2020 -0400 +++ b/nhmmer.xml Thu Jan 14 15:42:52 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@"> +<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy1"> <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description> <macros> <import>macros.xml</import> @@ -7,6 +7,7 @@ <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ +@ADDTHREADS@ nhmmer @OFORMAT_WITH_OPTS@