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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde |
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modified:
macros.xml readme.rst |
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added:
tool-data/hmm_database.loc.sample tool_data_table_conf.xml.sample |
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| diff -r f239ab5f45f4 -r d15979968b74 macros.xml --- a/macros.xml Sat Jun 25 15:07:17 2016 -0400 +++ b/macros.xml Mon Nov 14 15:11:53 2016 -0500 |
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| @@ -391,6 +391,32 @@ <param name="w_length" label="Window Length" help="(--w_length)" optional="True" type="integer" /> </xml> + <token name="@INPUTHMMCHOICE@"> +#if $input_hmm_conditional.input_hmm_source == "history": + '$input_hmm_conditional.hmmfile' +#else: + '$input_hmm_conditional.index.fields.db_path' +#end if + </token> + <xml name="input_hmm_choice"> + <conditional name="input_hmm_conditional"> + <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" > + <option value="indexed" selected="True">Use a built-in HMM model database</option> + <option value="history">Use a HMM database from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator"> + <options from_data_table="hmm_database"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> + </when> <!-- history --> + </conditional> <!-- input_hmm_conditional --> + </xml> <xml name="input_hmm"> <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> </xml> @@ -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 <http://selab.janelia.org/people/eddys/blog/?p=508>`__. +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. @@ -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/ ]]></token> |
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| diff -r f239ab5f45f4 -r d15979968b74 readme.rst --- a/readme.rst Sat Jun 25 15:07:17 2016 -0400 +++ b/readme.rst Mon Nov 14 15:11:53 2016 -0500 |
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| @@ -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 |
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| diff -r f239ab5f45f4 -r d15979968b74 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 15:11:53 2016 -0500 |
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| @@ -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): +# +#<unique_build_id> <display_name> <file_base_path> +# +#So, for example: +#pfam_a Pfam-a /data/db/pfam/Pfam-A.hmm |
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| diff -r f239ab5f45f4 -r d15979968b74 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 15:11:53 2016 -0500 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in the HMM database format --> + <table name="hmm_database" comment_char="#"> + <columns>value, name, db_path</columns> + <file path="tool-data/hmm_database.loc" /> + </table> +</tables> |