Mercurial > repos > devteam > picard

annotate picard_BedToIntervalList.xml @ 32:f9242e01365a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 2a17c789e0a5
children 3f254c5ced1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>convert coordinate data into picard interval list format</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 </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
7 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
10 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 #set $picard_dict = "localref.dict"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
13
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
14 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
15
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 #if str( $reference_source.reference_source_selector ) == "history":
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
17
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
21
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
22 &&
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
23
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 #else:
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
25
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa)
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
28
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
29 #end if
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
30
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
31 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 BedToIntervalList
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
33 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 OUTPUT="${outFile}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
35
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 SEQUENCE_DICTIONARY="${picard_dict}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
39
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
40 ]]></command>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
41
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
43
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <options from_data_table="picard_indexes">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 <filter type="sort_by" column="2" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 <validator type="no_options" message="No indexes are available" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 </when>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
58 <when value="history">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 <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" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 </conditional>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
62
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 </data>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
75 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
78
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
79
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 SEQUENCE_DICTIONARY=File
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93 SD=File The sequence dictionary. You can either use dictionary pre-cached
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 on this instance of Galaxy, or create one on teh fly from a FASTA
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95 file uploaded to history (right pane of the interface).
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
100 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101 </tool>