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comparison sortmerna.xml @ 5:cd8c76234b0c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5
author rnateam
date Wed, 31 May 2017 14:55:32 -0400
parents 1bdb57965c6f
children 185effcdfb68
comparison
equal deleted inserted replaced
4:1bdb57965c6f 5:cd8c76234b0c
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.2"> 1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3">
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>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="2.1b">sortmerna</requirement> 7 <requirement type="package" version="@VERSION@">sortmerna</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <regex match="This program builds a Burst trie on an input rRNA database" 10 <regex match="This program builds a Burst trie on an input rRNA database"
8 source="both" 11 source="both"
9 level="fatal" 12 level="fatal"
31 #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]
32 #set $sep = ':' 35 #set $sep = ':'
33 #end for 36 #end for
34 #else if str( $databases_type.databases_selector ) == 'cached_to_index' 37 #else if str( $databases_type.databases_selector ) == 'cached_to_index'
35 ## 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
36 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) 39 #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
37 #for $db in $databases_type.input_databases.value 40 #for $db in $databases_type.input_databases.value
38 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + '-reindexed' 41 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed'
39 #set $sep = ':' 42 #set $sep = ':'
40 #end for 43 #end for
41 #else: 44 #else:
42 ## 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
43 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) 46 #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
44 #for $db in $databases_type.input_databases.value 47 #for $db in $databases_type.input_databases.value
45 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] 48 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db]
46 #set $sep = ':' 49 #set $sep = ':'
47 #end for 50 #end for
48 #end if 51 #end if
49 52
50 #if str( $databases_type.databases_selector ) != 'cached': 53 #if str( $databases_type.databases_selector ) != 'cached':