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comparison sortmerna.xml @ 12:bf5dbe8f7d4c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 86b25c80bf4746a0bb73002040487242048a40d2-dirty
author bebatut
date Tue, 10 Nov 2015 04:05:25 -0500
parents b8ba70feb088
children 4016c1db6886
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11:b8ba70feb088 12:bf5dbe8f7d4c
9 <exit_code range="1:" /> 9 <exit_code range="1:" />
10 </stdio> 10 </stdio>
11 11
12 <version_command> 12 <version_command>
13 <![CDATA[ 13 <![CDATA[
14 sortmerna --version 2>&1|grep 'SortMeRNA version' 14 \${SORTMERNADIR}/sortmerna --version 2>&1|grep 'SortMeRNA version'
15 ]]> 15 ]]>
16 </version_command> 16 </version_command>
17 17
18 <command> 18 <command>
19 <![CDATA[ 19 <![CDATA[
32 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] 32 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0]
33 #set $sep = ':' 33 #set $sep = ':'
34 #end for 34 #end for
35 #end if 35 #end if
36 36
37 indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos 37 \${SORTMERNADIR}/indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos
38 38
39 && 39 &&
40 40
41 sortmerna 41 \${SORTMERNADIR}/sortmerna
42 --ref $ref 42 --ref $ref
43 --reads $input_sequence_file 43 --reads $input_sequence_file
44 --aligned aligned 44 --aligned aligned
45 45
46 $fastx.fastx_test 46 $fastx.fastx_test