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comparison picard_BedToIntervalList.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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children 3a3234d7a2e8
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="1.126.0">
2 <description>convert coordinate data into picard interval list format</description>
3 <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>
4
5 <macros>
6 <import>picard_macros.xml</import>
7 </macros>
8
9 <command>
10 @java_options@
11
12 #set $picard_dict = "localref.dict"
13 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
14
15 ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
16
17 #if str( $reference_source.reference_source_selector ) == "history":
18
19 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
20 QUIET=true
21 VERBOSITY=ERROR
22
23 &amp;&amp;
24
25 #else:
26
27 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa)
28 #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict
29
30 #end if
31
32 java -jar \$JAVA_JAR_PATH/picard.jar
33 BedToIntervalList
34 INPUT="${inputFile}"
35 OUTPUT="${outFile}"
36
37 SEQUENCE_DICTIONARY="${picard_dict}"
38 QUIET=true
39 VERBOSITY=ERROR
40
41 </command>
42
43 <inputs>
44
45 <conditional name="reference_source">
46 <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
47 <option value="cached">Local cache</option>
48 <option value="history">History</option>
49 </param>
50 <when value="cached">
51 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
52 <options from_data_table="picard_indexes">
53 <filter type="sort_by" column="2" />
54 <validator type="no_options" message="No indexes are available" />
55 </options>
56 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
57 </param>
58 </when>
59 <when value="history">
60 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
61 </when>
62 </conditional>
63
64 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" />
65
66 </inputs>
67 <outputs>
68 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
69 </data>
70 </outputs>
71 <tests>
72 <test>
73 <param name="reference_source_selector" value="history" />
74 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" />
75 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
76 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="2" />
77 </test>
78 </tests>
79
80 <stdio>
81 <exit_code range="1:" level="fatal"/>
82 </stdio>
83
84 <help>
85
86 .. class:: infomark
87
88 **Purpose**
89
90 Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format.
91
92 @dataset_collections@
93
94 @description@
95
96 SEQUENCE_DICTIONARY=File
97 SD=File The sequence dictionary. You can either use dictionary pre-cached
98 on this instance of Galaxy, or create one on teh fly from a FASTA
99 file uploaded to history (right pane of the interface).
100
101
102 @more_info@
103 </help>
104 </tool>
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