Mercurial > repos > devteam > picard
comparison picard_NormalizeFasta.xml @ 14:465cbb0cf2eb draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
| author | devteam |
|---|---|
| date | Wed, 07 Dec 2016 14:56:30 -0500 |
| parents | 7e6fd3d0f16e |
| children | 5053a18d9bc8 |
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| 13:7e6fd3d0f16e | 14:465cbb0cf2eb |
|---|---|
| 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 |