Mercurial > repos > rnateam > sortmerna
changeset 6:185effcdfb68 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf
| author | rnateam |
|---|---|
| date | Tue, 06 Jun 2017 13:41:03 -0400 |
| parents | cd8c76234b0c |
| children | 1eafcc450052 |
| files | sortmerna.xml tool-data/rRNA_databases.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/sortmerna.xml Wed May 31 14:55:32 2017 -0400 +++ b/sortmerna.xml Tue Jun 06 13:41:03 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3"> +<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4"> <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> <macros> <import>macros.xml</import> @@ -36,14 +36,14 @@ #end for #else if str( $databases_type.databases_selector ) == 'cached_to_index' ## databases path is not directly accessible, must match by hand with LOC file contents - #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) + #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) #for $db in $databases_type.input_databases.value #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed' #set $sep = ':' #end for #else: ## databases path is not directly accessible, must match by hand with LOC file contents - #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) + #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) #for $db in $databases_type.input_databases.value #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] #set $sep = ':'
--- a/tool-data/rRNA_databases.loc.sample Wed May 31 14:55:32 2017 -0400 +++ b/tool-data/rRNA_databases.loc.sample Tue Jun 06 13:41:03 2017 -0400 @@ -1,1 +1,1 @@ -#<unique_id> <database_caption> <name> <fasta_file_path> +#<unique_id> <database_caption> <fasta_file_path>
--- a/tool_data_table_conf.xml.sample Wed May 31 14:55:32 2017 -0400 +++ b/tool_data_table_conf.xml.sample Tue Jun 06 13:41:03 2017 -0400 @@ -1,7 +1,7 @@ <tables> <!-- Locations of public ribosomal databases --> <table name="rRNA_databases" comment_char="#"> - <columns>value, name, dbkey, path</columns> + <columns>value, name, path</columns> <file path="tool-data/rRNA_databases.loc" /> </table> </tables>