# HG changeset patch # User iuc # Date 1479154276 18000 # Node ID b49a4465041d7fb34af6bdac728d8eeff5851332 # Parent 216b19e6c31734f430d5a402806d54e59c6759d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde diff -r 216b19e6c317 -r b49a4465041d hmmscan.xml --- a/hmmscan.xml Sat Jun 25 15:06:16 2016 -0400 +++ b/hmmscan.xml Mon Nov 14 15:11:16 2016 -0500 @@ -1,5 +1,5 @@ - + search sequence(s) against a profile database macros.xml @@ -7,8 +7,10 @@ $output; -## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype -rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p; +@INPUTHMMCHOICE@ +'$seqfile' +> '$output' +#if $input_hmm_conditional.input_hmm_source == "history": + ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype + && rm '${input_hmm_conditional.hmmfile}.h3m' '${input_hmm_conditional.hmmfile}.h3i' '${input_hmm_conditional.hmmfile}.h3f' '${input_hmm_conditional.hmmfile}.h3p'; +#end if ]]> - + @@ -38,20 +42,21 @@ - - + + 'tblout' in oformat - + 'domtblout' in oformat - + 'pfamtblout' in oformat - + + diff -r 216b19e6c317 -r b49a4465041d macros.xml --- a/macros.xml Sat Jun 25 15:06:16 2016 -0400 +++ b/macros.xml Mon Nov 14 15:11:16 2016 -0500 @@ -391,6 +391,32 @@ + +#if $input_hmm_conditional.input_hmm_source == "history": + '$input_hmm_conditional.hmmfile' +#else: + '$input_hmm_conditional.index.fields.db_path' +#end if + + + + + + + + + + + + + + + + + + + + @@ -524,7 +550,7 @@ **Advanced Documentation** A more detailed look at the internals of the various filter pipelines was -posted on the `developer's blog `__. +posted on the `developer's blog `__. The information posted there may be useful to those who are struggling with poor-scoring sequences. @@ -1041,7 +1067,7 @@ Attribution ----------- -This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/ +This Galaxy tool relies on HMMER3_ Internally the software is cited as: :: @@ -1056,7 +1082,7 @@ documentation is copied from the HMMER3 documentation. .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0 -.. _HMMER3: http://hmmer.janelia.org/ +.. _HMMER3: http://hmmer.org/ ]]> diff -r 216b19e6c317 -r b49a4465041d readme.rst --- a/readme.rst Sat Jun 25 15:06:16 2016 -0400 +++ b/readme.rst Mon Nov 14 15:11:16 2016 -0500 @@ -29,6 +29,7 @@ History ======= +* v0.1.1 - hmmscan: add the possibility to scan a built-in hmm profile database * v0.1 - Initial public release diff -r 216b19e6c317 -r b49a4465041d tool-data/hmm_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hmm_database.loc.sample Mon Nov 14 15:11:16 2016 -0500 @@ -0,0 +1,10 @@ +#This is a sample file that enables the hmmer tools to find the HMM databases +#You will need to create these data files and then create +#a hmm_database.loc file similar to this one (store it in this directory) +#that points to the directories in which those files are stored. +#The hmm_database_indices.loc file has this format (longer white space characters are TAB characters): +# +# +# +#So, for example: +#pfam_a Pfam-a /data/db/pfam/Pfam-A.hmm diff -r 216b19e6c317 -r b49a4465041d tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Nov 14 15:11:16 2016 -0500 @@ -0,0 +1,7 @@ + + + + value, name, db_path + +
+