Mercurial > repos > devteam > ncbi_blast_plus
diff tools/ncbi_blast_plus/ncbi_macros.xml @ 27:6f8ea4b9a2c4 draft
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
author | peterjc |
---|---|
date | Wed, 09 Sep 2020 15:32:17 +0000 |
parents | 2889433c7ae1 |
children | 87a7ee4cb36f |
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--- a/tools/ncbi_blast_plus/ncbi_macros.xml Sat Jul 20 18:36:36 2019 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Sep 09 15:32:17 2020 +0000 @@ -1,5 +1,7 @@ <macros> - <token name="@WRAPPER_VERSION@">0.3.3</token> + <token name="@TOOL_VERSION@">2.7.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">16.10</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> @@ -7,7 +9,7 @@ <xml name="preamble"> <requirements> - <requirement type="package" version="2.7.1">blast</requirement> + <requirement type="package" version="@TOOL_VERSION@">blast</requirement> </requirements> <version_command>@BINARY@ -version</version_command> </xml> @@ -426,14 +428,40 @@ <option value="prot">Protein</option> </param> <when value="nucl"> - <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> - <options from_data_table="blastdb" /> - </param> + <conditional name="db_origin"> + <param name="db_origin_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="true">Locally installed BLAST database</option> + <option value="histdb">BLAST database from your history</option> + </param> + <when value="db"> + <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> + <options from_data_table="blastdb" /> + </param> + <param name="histdb" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> + </when> + </conditional> </when> <when value="prot"> - <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database"> - <options from_data_table="blastdb_p" /> - </param> + <conditional name="db_origin"> + <param name="db_origin_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="true">Locally installed BLAST database</option> + <option value="histdb">BLAST database from your history</option> + </param> + <when value="db"> + <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database"> + <options from_data_table="blastdb_p" /> + </param> + <param name="histdb" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> + </when> + </conditional> </when> </conditional> </xml> @@ -574,6 +602,17 @@ #end if ]]></token> + <!-- Implement -dbtype and -db command line options (in blastdbcmd) --> + <token name="@DBCMD_OPTS@"><![CDATA[ +-dbtype "$db_opts.db_type" +#if $db_opts.db_origin.db_origin_selector=="db": + -db "${db_opts.db_origin.database.fields.path.replace(',',' ')}" +#else if $db_opts.db_origin.db_origin_selector=="histdb": + -db '${os.path.join($db_opts.db_origin.histdb.extra_files_path, "blastdb")}' +#end if + ]]></token> + + <!-- Implement -db ... / -subject ... command line options --> <token name="@BLAST_DB_SUBJECT@"><![CDATA[ #if $db_opts.db_opts_selector == "db": -db '${" ".join(str($db_opts.database.fields.path).split(","))}' @@ -699,6 +738,15 @@ #end if ]]></token> + <!-- @ON_DBCMD_OPTS@ is for use with @DBCMD_OPTS@ --> + <token name="@ON_DBCMD_OPTS@"><![CDATA[ +#if str($db_opts.db_origin.db_origin_selector)=="db" +'${db_opts.db_origin.database}' +#else +'${db_opts.db_origin.histdb.name}' +#end if +]]></token> + <token name="@REFERENCES@"><![CDATA[ Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39