Mercurial > repos > devteam > picard
annotate picard_NormalizeFasta.xml @ 12:05087b27692a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
| author | devteam |
|---|---|
| date | Sun, 27 Nov 2016 15:11:50 -0500 |
| parents | 3a3234d7a2e8 |
| children | 7e6fd3d0f16e |
| rev | line source |
|---|---|
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
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changeset
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1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>normalize fasta datasets</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
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6 <expand macro="requirements" /> |
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12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
7 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 8 @java_options@ |
| 9 | |
| 10 | |
| 11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa | |
| 12 #set $fasta_file="local_fasta.fa" | |
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12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
13 ln -s "${inputFile}" "${fasta_file}" && |
| 5 | 14 |
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12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
15 picard |
| 5 | 16 NormalizeFasta |
| 17 | |
| 18 INPUT="${fasta_file}" | |
| 19 OUTPUT="${outFile}" | |
| 20 LINE_LENGTH="${line_length}" | |
| 21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}" | |
| 22 | |
| 23 QUIET=true | |
| 24 VERBOSITY=ERROR | |
| 25 | |
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12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
26 ]]></command> |
| 5 | 27 <inputs> |
| 28 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" /> | |
| 29 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/> | |
| 30 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/> | |
| 31 </inputs> | |
| 32 | |
| 33 <outputs> | |
| 34 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/> | |
| 35 </outputs> | |
| 36 | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/> | |
| 40 <param name="line_length" value="40"/> | |
| 41 <param name="truncate_sequence_names_at_whitespaces" value="False"/> | |
| 42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/> | |
| 43 </test> | |
| 44 </tests> | |
| 45 | |
| 46 | |
| 47 <help> | |
| 48 | |
| 49 **Purpose** | |
| 50 | |
| 51 Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length. | |
| 52 | |
| 53 @dataset_collections@ | |
| 54 | |
| 55 @description@ | |
| 56 | |
| 57 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100. | |
| 58 | |
| 59 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean | |
| 60 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false} | |
| 61 | |
| 62 @more_info@ | |
| 63 | |
| 64 </help> | |
| 65 </tool> | |
| 66 | |
| 67 |