picard: picard_MergeBamAlignment.xml annotate

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

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>

Mercurial > repos > devteam > picard

annotate picard_MergeBamAlignment.xml @ 25:7d34178f2812 draft