annotate picard_NormalizeFasta.xml @ 9:5eaa8a968300 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author devteam
date Fri, 09 Oct 2015 17:43:13 -0400
parents 3a3234d7a2e8
children 05087b27692a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.0">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>normalize fasta datasets</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
6 <expand macro="requirements" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
7 <command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 #set $fasta_file="local_fasta.fa"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 ln -s "${inputFile}" "${fasta_file}" &amp;&amp;
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 NormalizeFasta
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 INPUT="${fasta_file}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 LINE_LENGTH="${line_length}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <param name="line_length" value="40"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 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.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70