annotate picard_MergeBamAlignment.xml @ 25:7d34178f2812 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b
author iuc
date Tue, 11 Jun 2019 02:36:54 -0400
parents 2a17c789e0a5
children 585027e65f3b
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: 13
diff changeset
1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>merge alignment data with additional info stored in an unmapped 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: 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: 9
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 #set $picard_dict = "localref.dict"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
12
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
13 ln -s "${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
14
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 #if str( $reference_source.reference_source_selector ) == "history":
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
16
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 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
20 @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
21
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
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( $reference_source.ref_file.fields.path )
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
27
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
29
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
30 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 MergeBamAlignment
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 UNMAPPED_BAM="${unmapped_bam}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
33
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}
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 #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file":
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 #for $dataset in $aligned_or_read1_and_read2.aligned_bams:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 ALIGNED_BAM="${dataset.aligned_bam}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files":
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams:
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
45 READ2_ALIGNED_BAM="${dataset.read2_aligned_bam}"
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 #else
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 #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
52
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 REFERENCE_SEQUENCE="${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
55
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 CLIP_ADAPTERS="${clip_adapters}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 ALIGNED_READS_ONLY="${aligned_reads_only}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
60
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 #for $attribute in $attributes_to_retain:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 ATTRIBUTES_TO_RETAIN="${$attribute.attribute}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 #end for
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
64
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 #for $attribute in $attributes_to_remove:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 ATTRIBUTES_TO_REMOVE="${$attribute.attribute}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 #end for
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
68
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 READ1_TRIM="${read1_trim}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 READ2_TRIM="${read2_trim}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
71
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 #if str( $orientations ) != "None":
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 #for $orientation in str( $orientations ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 EXPECTED_ORIENTATIONS="${orientation}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 #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
77
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
78 ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}"
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 CLIP_OVERLAPPING_READS="${clip_overlapping_reads}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 ADD_MATE_CIGAR="${add_mate_cigar}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
83
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 SORT_ORDER=coordinate
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 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
89 @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
90
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
91 ]]></command>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
92
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93 <inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
94
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 <options from_data_table="picard_indexes">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 <filter type="sort_by" column="2" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104 <validator type="no_options" message="No indexes are available" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106 <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
107 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108 </when>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
109 <when value="history">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110 <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
111 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
112 </conditional>
13
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:
diff changeset
114 <param format="sam,bam" name="unmapped_bam" type="data" label="Selected unaligned SAM or BAM with original reads" help="UNMAPPED_BAM; This dataset must be sorted in queryname order (use picard_SortSam to do this)" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
115 <conditional name="aligned_or_read1_and_read2">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
116 <param name="aligned_or_read1_and_read2_selector" type="select" label="What type of aligned data do you have?">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
117 <option value="paired_one_file">Paired data in a single BAM file (ALIGNED_BAM)</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
118 <option value="paired_two_files">Paired data in separate files (READ1_ALIGNED_BAM and READ2_ALIGNED_BAM)</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
119 <option value="single_file">Singe end data (READ1_ALIGNED_BAM)</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
120 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
121 <when value="paired_one_file">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
122 <repeat name="aligned_bams" title="Aligned SAM or BAM dataset" min="1" help="You can provide multiple datasets">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
123 <param name="aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="ALIGNED_BAM"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
124 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
125 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
126 <when value="paired_two_files">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
127 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Read 1" min="1" help="You can provide multiple datasets">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
128 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read1" help="READ1_ALIGNED_BAM"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
129 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
130 <repeat name="read2_aligned_bams" title="Aligned SAM or BAM dataset for Read 2" min="1" help="You can provide multiple datasets">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
131 <param name="read2_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read2" help="READ2_ALIGNED_BAM"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
132 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
133 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
134 <when value="single_file">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
135 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Single Reads" min="1" help="You can provide multiple datasets">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
136 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="READ1_ALIGNED_BAM"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
137 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
138 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
139 </conditional>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
140
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
141 <param name="clip_adapters" type="boolean" checked="true" label="Whether to clip adapters where identified" help="CLIP_ADAPTERS; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
142 <param name="is_bisulfite_sequence" type="boolean" label="Whether the data is from bisulfite sequencing (used when caculating the NM tag)" help="IS_BISULFITE_SEQUENCE; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
143 <param name="aligned_reads_only" type="boolean" label="Whether to output only aligned reads" help="ALIGNED_READS_ONLY; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
144 <param name="max_insertions_or_deletions" type="integer" value="1" label="The maximum number of insertions or deletions permitted for an alignment to be included" help="MAX_INSERTIONS_OR_DELETIONS; Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. default=1"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
145
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
146 <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes">
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
147 <param name="attribute" type="text" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
148 </repeat>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
149
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
150 <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes">
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
151 <param name="attribute" type="text" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
152 </repeat>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
153
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
154 <param name="read1_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 1 prior to alignment" help="READ1_TRIM; default=0"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
155 <param name="read2_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 2 prior to alignment" help="READ2_TRIM; default=0"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
156
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
157 <param name="orientations" type="select" multiple="True" display="checkboxes" label="The expected orientation of proper read pairs" help="EXPECTED_ORIENTATIONS; multiple orinetations can be selected">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
158 <option value="FR">Forward/Reverse (FR)</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
159 <option value="RF">Reverse/Forward (RF)</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
160 <option value="TANDEM">Tandem</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
161 </param>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
162
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
163
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
164 <param name="aligner_proper_pair_flags" type="boolean" label="Use the aligner's idea of what a proper pair is rather than computing in this program" help="ALIGNER_PROPER_PAIR_FLAGS; default=False"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
165
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
166 <param name="primary_alignment_strategy" type="select" label="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragments" help="PRIMARY_ALIGNMENT_STRATEGY; see help below for more info; default=BestMapq">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
167 <option value="BestMapq" selected="True">BestMapq</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
168 <option value="EarliestFragment">EarliestFragment</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
169 <option value="BestEndMapq">BestEndMapq</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
170 <option value="MostDistant">MostDistant</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
171 </param>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
172
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
173 <param name="clip_overlapping_reads" type="boolean" checked="True" label="For paired reads, soft clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate" help="CLIP_OVERLAPPING_READS; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
174 <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
175 <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
176 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
177 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
178 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
179 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
180 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
181 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
182 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
183 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
184 <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
185 <param name="unmapped_bam" value="picard_MergeBamAlignment_unaligned.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
186 <param name="aligned_or_read1_and_read2_selector" value="paired_one_file"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
187 <param name="aligned_bam" value="picard_MergeBamAlignment_aligned.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
188 <param name="clip_adapters" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
189 <param name="is_bisulfite_sequence" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
190 <param name="aligned_reads_only" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
191 <param name="max_insertions_or_deletions" value="1"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
192 <param name="read1_trim" value="0"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
193 <param name="read2_trim" value="0"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
194 <param name="orientation" value="FR"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
195 <param name="aligner_proper_pair_flags" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
196 <param name="primary_alignment_strategy" value="BestMapq"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
197 <param name="clip_overlapping_reads" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
198 <param name="include_secondary_alignments" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
199 <param name="add_mate_cigar" value="True"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
200 <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
201 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
202 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
203
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
204
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
205 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
206
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
207 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
208
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
209 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
210
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
211 Merges alignment data from a SAM or BAM dataset with additional data stored in an unmapped BAM dataset and produces a third SAM or BAM dataset of aligned and unaligned reads.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
212
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
213 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
214
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
215 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
216
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
217 UNMAPPED_BAM=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
218 UNMAPPED=File Original SAM or BAM file of unmapped reads, which must be in queryname order. Required.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
219
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
220 ALIGNED_BAM=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
221 ALIGNED=File SAM or BAM file(s) with alignment data. This option may be specified 0 or more times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
222 Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED)
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
223 READ2_ALIGNED_BAM (R2_ALIGNED)
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
224
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
225 READ1_ALIGNED_BAM=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
226 R1_ALIGNED=File SAM or BAM file(s) with alignment data from the first read of a pair. This option may be
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
227 specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
228 (ALIGNED)
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
229
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
230 READ2_ALIGNED_BAM=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
231 R2_ALIGNED=File SAM or BAM file(s) with alignment data from the second read of a pair. This option may
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
232 be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
233 (ALIGNED)
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
234
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
235 PAIRED_RUN=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
236 PE=Boolean This argument is ignored and will be removed. Required. 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
237
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
238 JUMP_SIZE=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
239 JUMP=Integer The expected jump size (required if this is a jumping library). Deprecated. Use
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
240 EXPECTED_ORIENTATIONS instead Default value: null. Cannot be used in conjuction with
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
241 option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS)
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
242
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
243 CLIP_ADAPTERS=Boolean Whether to clip adapters where identified. Default value: true. 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
244
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
245 IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag). Default value:
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
246 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
247
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
248 ALIGNED_READS_ONLY=Boolean Whether to output only aligned reads. 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
249
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
250 MAX_INSERTIONS_OR_DELETIONS=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
251 MAX_GAPS=Integer The maximum number of insertions or deletions permitted for an alignment to be included.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
252 Alignments with more than this many insertions or deletions will be ignored. Set to -1 to
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
253 allow any number of insertions or deletions. Default value: 1.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
254
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
255 ATTRIBUTES_TO_RETAIN=String Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
256 from the alignment data when merging. This option may be specified 0 or more times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
257
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
258 ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
259 ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
260 times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
261
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
262 READ1_TRIM=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
263 R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
264 value: 0.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
265
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
266 READ2_TRIM=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
267 R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
268 value: 0.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
269
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
270 EXPECTED_ORIENTATIONS=PairOrientation
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
271 ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR,
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
272 RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
273 with option(s) JUMP_SIZE (JUMP)
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
274
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
275 ALIGNER_PROPER_PAIR_FLAGS=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
276 Use the aligner's idea of what a proper pair is rather than computing in this program.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
277 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
278
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
279 SORT_ORDER=SortOrder
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
280 SO=SortOrder The order in which the merged reads should be output. Default value: coordinate.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
281 Possible values: {unsorted, queryname, coordinate}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
282
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
283 PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
284 Strategy for selecting primary alignment when the aligner has provided more than one
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
285 alignment for a pair or fragment, and none are marked as primary, more than one is marked
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
286 as primary, or the primary alignment is filtered out for some reason. BestMapq expects
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
287 that multiple alignments will be correlated with HI tag, and prefers the pair of
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
288 alignments with the largest MAPQ, in the absence of a primary selected by the aligner.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
289 EarliestFragment prefers the alignment which maps the earliest base in the read. Note
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
290 that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
291 cases in which the aligner is not pair-aware, and does not output the HI tag. It simply
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
292 picks the alignment for each end with the highest MAPQ, and makes those alignments
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
293 primary, regardless of whether the two alignments make sense together.MostDistant is also
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
294 for a non-pair-aware aligner, and picks the alignment pair with the largest insert size.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
295 If all alignments would be chimeric, it picks the alignments for each end with the best
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
296 MAPQ. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
297 Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
298
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
299 CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
300 extend past the 5' end of its mate. Default value: true. 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
301
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
302 INCLUDE_SECONDARY_ALIGNMENTS=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
303 If false, do not write secondary alignments to output. Default value: true.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
304 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
305
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
306 ADD_MATE_CIGAR=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
307 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
308
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
309
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
310
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
311
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
312 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
313 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 13
diff changeset
314 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
315 </tool>