Mercurial > repos > iuc > hmmer_jackhmmer
changeset 6:d9ce554da9b4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
| author | iuc |
|---|---|
| date | Thu, 14 Jan 2021 15:38:47 +0000 |
| parents | 5113c71c7031 |
| children | 6e27bb3f0fa6 |
| files | jackhmmer.xml macros.xml |
| diffstat | 2 files changed, 8 insertions(+), 4 deletions(-) [+] |
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--- a/jackhmmer.xml Tue Jun 16 05:32:33 2020 -0400 +++ b/jackhmmer.xml Thu Jan 14 15:38:47 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@"> +<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy1"> <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description> <macros> <import>macros.xml</import> @@ -7,6 +7,7 @@ <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ +@ADDTHREADS@ jackhmmer -N $N @OFORMAT_WITH_OPTS@
--- a/macros.xml Tue Jun 16 05:32:33 2020 -0400 +++ b/macros.xml Thu Jan 14 15:38:47 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