Mercurial > repos > devteam > picard

annotate picard_ValidateSamFile.xml @ 29:1aac2a13842a 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 1ef1c65fa4d78e1332411af1999862d5a8f28125"
author iuc
date Sun, 20 Mar 2022 14:06:40 +0000
parents 881d7645d1bf
children b502c227b5e6
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="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>assess validity of SAM/BAM dataset</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: 7
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 <stdio>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
9 <exit_code range="1:" level="warning"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
10 </stdio>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
11 <command><![CDATA[
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
12
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
14
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
15 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
16
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
17 &&
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
18
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 ##set up input files
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
20 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 #set $reference_fasta_filename = "localref.fa"
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
22
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 #if str( $reference_source.reference_source_selector ) == "history":
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
24 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 #else:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 #end if
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
28
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 @java_options@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
30
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
31 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 ValidateSamFile
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
33
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
34 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 MODE="${mode}"
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
37
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 #if str( $ignore ) != "None":
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 IGNORE="${element}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 #end if
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
43
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 MAX_OUTPUT="${max_output}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 IGNORE_WARNINGS="${ignore_warnings}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
49
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 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
51 @TMPDIR_OPTION@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 QUIET=true
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
53
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
54 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <options from_data_table="picard_indexes">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <filter type="sort_by" column="2" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <validator type="no_options" message="No indexes are available" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <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
69 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 </when>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
71 <when value="history">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <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
73 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 </conditional>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
75
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <param name="mode" type="select" label="Select output mode" help="MODE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <option value="VERBOSE">Verbose</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <option value="SUMMARY">Summary</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
28
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
83 <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
84 <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
85 <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
86 <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
87 <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
88 <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
89 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
90 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
91 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
92 <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
93 <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
94 <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
95 <option value="INVALID_CIGAR">INVALID_CIGAR</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
96 <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
97 <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
98 <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
99 <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
100 <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
101 <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
102 <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
103 <option value="INVALID_TAG_NM">INVALID_TAG_NM</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
104 <option value="MISSING_TAG_NM">MISSING_TAG_NM</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
105 <option value="MISSING_HEADER">MISSING_HEADER</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
106 <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
107 <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
108 <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
109 <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
110 <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
111 <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
112 <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
113 <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
114 <option value="TRUNCATED_FILE">TRUNCATED_FILE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
115 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
116 <option value="EMPTY_READ">EMPTY_READ</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
117 <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
118 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
119 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
120 <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
121 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
122 <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
123 <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
124 <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
125 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
126 <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
127 <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
128 <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
129 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
130 <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
131 <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
132 <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
133 <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
134 <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
135 <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
136 <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option>
881d7645d1bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
iuc
parents: 20
diff changeset
137 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
138 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
139 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
140 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
141 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
142 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
143
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
144 </inputs>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
145
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
146 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
147 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
148 </outputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
149
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
150 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
151 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
152 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
153 <param name="reference_source_selector" value="history"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
154 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
155 <param name="mode" value="VERBOSE"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
156 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
157 <param name="max_output" value="100"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
158 <param name="ignore_warnings" value="Fasle"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
159 <param name="validate_index" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
160 <param name="is_bisulfite_sequenced" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
161 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
162 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
163 </tests>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
164
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
165 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
166
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
167 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
168
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
169 Reads a SAM/BAM dataset and report on its validity.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
170
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
171 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
172
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
173 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
174
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
175 MODE=Mode
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
176 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
177 default value. Possible values: {VERBOSE, SUMMARY}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
178
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
179 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
180 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
181 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
182 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
183 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
184 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
185 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
186 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
187 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
188 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
189 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
190 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
191 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
192 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
193 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
194 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
195 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
196 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
197 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
198 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
199 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
200 specified 0 or more times.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
201
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
202 MAX_OUTPUT=Integer
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
203 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
204 be set to 'null' to clear the default value.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
205
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
206 REFERENCE_SEQUENCE=File
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
207 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
208 value: null.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
209
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
210 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
211 be set to 'null' to clear the default value. Possible values: {true, false}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
212
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
213 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
214 value: true. This option can be set to 'null' to clear the default value. Possible
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
215 values: {true, false}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
216
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
217 IS_BISULFITE_SEQUENCED=Boolean
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
218 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
219 counted as an error in computing the value of the NM tag. Default value: false. This
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
220 option can be set to 'null' to clear the default value. Possible values: {true, false}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
221
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
222 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
223
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
224 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
225 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
226 </tool>