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comparison sortmerna.xml @ 6:185effcdfb68 draft

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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
comparison
equal deleted inserted replaced
5:cd8c76234b0c 6:185effcdfb68
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3"> 1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4">
2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> 2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
34 #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0] 34 #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
35 #set $sep = ':' 35 #set $sep = ':'
36 #end for 36 #end for
37 #else if str( $databases_type.databases_selector ) == 'cached_to_index' 37 #else if str( $databases_type.databases_selector ) == 'cached_to_index'
38 ## databases path is not directly accessible, must match by hand with LOC file contents 38 ## databases path is not directly accessible, must match by hand with LOC file contents
39 #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) 39 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
40 #for $db in $databases_type.input_databases.value 40 #for $db in $databases_type.input_databases.value
41 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed' 41 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed'
42 #set $sep = ':' 42 #set $sep = ':'
43 #end for 43 #end for
44 #else: 44 #else:
45 ## databases path is not directly accessible, must match by hand with LOC file contents 45 ## databases path is not directly accessible, must match by hand with LOC file contents
46 #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) 46 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
47 #for $db in $databases_type.input_databases.value 47 #for $db in $databases_type.input_databases.value
48 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] 48 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db]
49 #set $sep = ':' 49 #set $sep = ':'
50 #end for 50 #end for
51 #end if 51 #end if