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comparison picard_NormalizeFasta.xml @ 9:41b8d087a2d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
author devteam
date Wed, 07 Dec 2016 14:56:16 -0500
parents e417b1d6288d
children 486d7500da69
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8:e417b1d6288d 9:41b8d087a2d2
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
10 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa 10 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
11 ln -s '$inputFile' '$inputFile.element_identifier'.fa && 11 #import re
12 12 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
13 ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
13 picard 14 picard
14 NormalizeFasta 15 NormalizeFasta
15 16
16 INPUT='$inputFile.element_identifier'.fa 17 INPUT='$escaped_element_identifier'.fa
17 OUTPUT="${outFile}" 18 OUTPUT="${outFile}"
18 LINE_LENGTH="${line_length}" 19 LINE_LENGTH="${line_length}"
19 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}" 20 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
20 21
21 QUIET=true 22 QUIET=true