Mercurial > repos > devteam > picard

annotate picard_ReorderSam.xml @ 28:881d7645d1bf 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 92e89c89178482870c14cf15f38fbfd4470aa130"
author iuc
date Sat, 15 Jan 2022 12:39:30 +0000
parents 2a17c789e0a5
children f9242e01365a
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="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
28
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
2 <description>reorder reads to match ordering in reference sequences</description>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
3 <macros>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
4 <import>picard_macros.xml</import>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
6 </macros>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
7 <xrefs>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
8 <xref type="bio.tools">picard_reordersam</xref>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
9 </xrefs>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
10 <expand macro="requirements" />
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
12 @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
13 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
14 #set $picard_dict = "localref.dict"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
15 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
16
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
17 ln -s "${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
18
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
19 #if str( $reference_source.reference_source_selector ) == "history":
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
20
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
21 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
22 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
23 VERBOSITY=ERROR
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
24 @TMPDIR_OPTION@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
25
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
26 &&
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
27
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
28 #else:
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
29
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
30 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
31
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
32 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
33
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
34 picard
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
35 ReorderSam
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
36 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
37 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
38 REFERENCE="${ref_fasta}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
39 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
40 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
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: 2
diff changeset
42 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
43 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
44 VERBOSITY=ERROR
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
45 @TMPDIR_OPTION@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
46
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
47 ]]></command>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
48
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
49 <inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
50
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
51 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
52 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
53 <option value="cached">Local cache</option>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
54 <option value="history">History</option>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
55 </param>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
56 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
57 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
58 <options from_data_table="picard_indexes">
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
59 <filter type="sort_by" column="2" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
60 <validator type="no_options" message="No indexes are available" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
61 </options>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
62 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
63 </param>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
64 </when>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
65 <when value="history">
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
66 <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" />
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
67 </when>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
68 </conditional>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
69
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
70 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
71 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
72 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
73 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
74
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
75 </inputs>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
76 <outputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
77 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
78 </outputs>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
79 <tests>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
80 <test>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
81 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
82 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
83 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
84 <param name="allow_incomplete_dict_concordance" value="false"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
85 <param name="allow_contig_length_discordance" value="false"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
86 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
87 </test>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
88 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
89
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
90
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
91 <help>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
92
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
93 .. class:: infomark
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
94
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
95 **Purpose**
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
96
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
97 ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
98
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
99 @dataset_collections@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
100
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
101 ----
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
102
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
103 .. class:: warningmark
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
104
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
105 Not to be confused with **SortSam**.
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
106
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
107 @description@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
108
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
109 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
110 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
111 sequence contigs. By default, this tool requires a corresponding contig in the new
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
112 reference for each read contig Default value: false. Possible values: {true, false}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
113
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
114 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
115 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
116 name but a different length. Highly dangerous, only use if you know what you are doing.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
117 Default value: false. Possible values: {true, false}
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
118
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
119 @more_info@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
120 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
121 <expand macro="citations" />
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
122 </tool>