Mercurial > repos > avowinkel > picard
diff picard_MergeBamAlignment.xml @ 0:5166ed57b1c4 draft
Uploaded version 1.135
| author | avowinkel |
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| date | Mon, 06 Jul 2015 14:46:32 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MergeBamAlignment.xml Mon Jul 06 14:46:32 2015 -0400 @@ -0,0 +1,327 @@ +<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="1.126.1"> + <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> + <macros> + <import>picard_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + @java_options@ + #set $picard_dict = "localref.dict" + #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension + + ln -s "${reference_source.ref_file}" "${ref_fasta}" && + + #if str( $reference_source.reference_source_selector ) == "history": + + java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" + QUIET=true + VERBOSITY=ERROR + + && + + #else: + + #set $ref_fasta = str( $reference_source.ref_file.fields.path ) + + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + MergeBamAlignment + UNMAPPED_BAM="${unmapped_bam}" + + PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false} + + #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file": + #for $dataset in $aligned_or_read1_and_read2.aligned_bams: + ALIGNED_BAM="${dataset.aligned_bam}" + #end for + #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files": + #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: + READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" + #end for + #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams: + READ2_ALIGNED_BAM="${dataset.read2_aligned_bam}" + #end for + #else + #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: + READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" + #end for + #end if + + OUTPUT="${outFile}" + REFERENCE_SEQUENCE="${ref_fasta}" + + CLIP_ADAPTERS="${clip_adapters}" + IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}" + ALIGNED_READS_ONLY="${aligned_reads_only}" + MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}" + + #for $attribute in $attributes_to_retain: + ATTRIBUTES_TO_RETAIN="${$attribute.attribute}" + #end for + + #for $attribute in $attributes_to_remove: + ATTRIBUTES_TO_REMOVE="${$attribute.attribute}" + #end for + + READ1_TRIM="${read1_trim}" + READ2_TRIM="${read2_trim}" + + #if str( $orientations ) != "None": + #for $orientation in str( $orientations ).split(','): ## See trello card https://trello.com/c/9nW02Zhd + EXPECTED_ORIENTATIONS="${orientation}" + #end for + #end if + + ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}" + PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}" + CLIP_OVERLAPPING_READS="${clip_overlapping_reads}" + INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}" + ADD_MATE_CIGAR="${add_mate_cigar}" + + VALIDATION_STRINGENCY="${validation_stringency}" + + SORT_ORDER=coordinate + QUIET=true + VERBOSITY=ERROR + + </command> + + <inputs> + + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> + <options from_data_table="picard_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <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" /> + </when> + </conditional> + + <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)" /> + <conditional name="aligned_or_read1_and_read2"> + <param name="aligned_or_read1_and_read2_selector" type="select" label="What type of aligned data do you have?"> + <option value="paired_one_file">Paired data in a single BAM file (ALIGNED_BAM)</option> + <option value="paired_two_files">Paired data in separate files (READ1_ALIGNED_BAM and READ2_ALIGNED_BAM)</option> + <option value="single_file">Singe end data (READ1_ALIGNED_BAM)</option> + </param> + <when value="paired_one_file"> + <repeat name="aligned_bams" title="Aligned SAM or BAM dataset" min="1" help="You can provide multiple datasets"> + <param name="aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="ALIGNED_BAM"/> + </repeat> + </when> + <when value="paired_two_files"> + <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Read 1" min="1" help="You can provide multiple datasets"> + <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"/> + </repeat> + <repeat name="read2_aligned_bams" title="Aligned SAM or BAM dataset for Read 2" min="1" help="You can provide multiple datasets"> + <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"/> + </repeat> + </when> + <when value="single_file"> + <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Single Reads" min="1" help="You can provide multiple datasets"> + <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="READ1_ALIGNED_BAM"/> + </repeat> + </when> + </conditional> + + <param name="clip_adapters" type="boolean" checked="true" label="Whether to clip adapters where identified" help="CLIP_ADAPTERS; default=True"/> + <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"/> + <param name="aligned_reads_only" type="boolean" label="Whether to output only aligned reads" help="ALIGNED_READS_ONLY; default=False"/> + <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"/> + + <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes"> + <param name="attribute" type="text" size="4" 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"/> + </repeat> + + <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes"> + <param name="attribute" type="text" size="4" 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"/> + </repeat> + + <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"/> + <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"/> + + <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"> + <option value="FR">Forward/Reverse (FR)</option> + <option value="RF">Reverse/Forward (RF)</option> + <option value="TANDEM">Tandem</option> + </param> + + + <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"/> + + <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"> + <option value="BestMapq" selected="True">BestMapq</option> + <option value="EarliestFragment">EarliestFragment</option> + <option value="BestEndMapq">BestEndMapq</option> + <option value="MostDistant">MostDistant</option> + </param> + + <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"/> + <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"/> + <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"/> + <expand macro="VS" /> + </inputs> + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" /> + <param name="unmapped_bam" value="picard_MergeBamAlignment_unaligned.bam" ftype="bam"/> + <param name="aligned_or_read1_and_read2_selector" value="paired_one_file"/> + <param name="aligned_bam" value="picard_MergeBamAlignment_aligned.bam" ftype="bam"/> + <param name="clip_adapters" value="True"/> + <param name="is_bisulfite_sequence" value="False"/> + <param name="aligned_reads_only" value="False"/> + <param name="max_insertions_or_deletions" value="1"/> + <param name="read1_trim" value="0"/> + <param name="read2_trim" value="0"/> + <param name="orientation" value="FR"/> + <param name="aligner_proper_pair_flags" value="False"/> + <param name="primary_alignment_strategy" value="BestMapq"/> + <param name="clip_overlapping_reads" value="True"/> + <param name="include_secondary_alignments" value="True"/> + <param name="add_mate_cigar" value="True"/> + <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +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. + +@dataset_collections@ + +@description@ + + UNMAPPED_BAM=File + UNMAPPED=File Original SAM or BAM file of unmapped reads, which must be in queryname order. Required. + + ALIGNED_BAM=File + ALIGNED=File SAM or BAM file(s) with alignment data. This option may be specified 0 or more times. + Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED) + READ2_ALIGNED_BAM (R2_ALIGNED) + + READ1_ALIGNED_BAM=File + R1_ALIGNED=File SAM or BAM file(s) with alignment data from the first read of a pair. This option may be + specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM + (ALIGNED) + + READ2_ALIGNED_BAM=File + R2_ALIGNED=File SAM or BAM file(s) with alignment data from the second read of a pair. This option may + be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM + (ALIGNED) + + PAIRED_RUN=Boolean + PE=Boolean This argument is ignored and will be removed. Required. Possible values: {true, false} + + JUMP_SIZE=Integer + JUMP=Integer The expected jump size (required if this is a jumping library). Deprecated. Use + EXPECTED_ORIENTATIONS instead Default value: null. Cannot be used in conjuction with + option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS) + + CLIP_ADAPTERS=Boolean Whether to clip adapters where identified. Default value: true. Possible values: {true, false} + + IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag). Default value: + false. Possible values: {true, false} + + ALIGNED_READS_ONLY=Boolean Whether to output only aligned reads. Default value: false. Possible values: {true, false} + + MAX_INSERTIONS_OR_DELETIONS=Integer + MAX_GAPS=Integer The maximum number of insertions or deletions permitted for an alignment to be included. + Alignments with more than this many insertions or deletions will be ignored. Set to -1 to + allow any number of insertions or deletions. Default value: 1. + + ATTRIBUTES_TO_RETAIN=String Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over + from the alignment data when merging. This option may be specified 0 or more times. + + ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides + ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more + times. + + READ1_TRIM=Integer + R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default + value: 0. + + READ2_TRIM=Integer + R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default + value: 0. + + EXPECTED_ORIENTATIONS=PairOrientation + ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR, + RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction + with option(s) JUMP_SIZE (JUMP) + + ALIGNER_PROPER_PAIR_FLAGS=Boolean + Use the aligner's idea of what a proper pair is rather than computing in this program. + Default value: false. Possible values: {true, false} + + SORT_ORDER=SortOrder + SO=SortOrder The order in which the merged reads should be output. Default value: coordinate. + Possible values: {unsorted, queryname, coordinate} + + PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy + Strategy for selecting primary alignment when the aligner has provided more than one + alignment for a pair or fragment, and none are marked as primary, more than one is marked + as primary, or the primary alignment is filtered out for some reason. BestMapq expects + that multiple alignments will be correlated with HI tag, and prefers the pair of + alignments with the largest MAPQ, in the absence of a primary selected by the aligner. + EarliestFragment prefers the alignment which maps the earliest base in the read. Note + that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for + cases in which the aligner is not pair-aware, and does not output the HI tag. It simply + picks the alignment for each end with the highest MAPQ, and makes those alignments + primary, regardless of whether the two alignments make sense together.MostDistant is also + for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. + If all alignments would be chimeric, it picks the alignments for each end with the best + MAPQ. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq. + Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant} + + CLIP_OVERLAPPING_READS=BooleanFor 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. Default value: true. Possible values: {true, false} + + INCLUDE_SECONDARY_ALIGNMENTS=Boolean + If false, do not write secondary alignments to output. Default value: true. + Possible values: {true, false} + + ADD_MATE_CIGAR=Boolean + MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false} + + + + +@more_info@ + </help> +</tool> + + + + + + + + + + + + +