Mercurial > repos > rnateam > sortmerna
comparison sortmerna.xml @ 5:cd8c76234b0c draft
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 |
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| 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': |