picard: picard_MergeBamAlignment.xml comparison

comparison picard_MergeBamAlignment.xml @ 13:7e6fd3d0f16e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

author	devteam
date	Tue, 06 Dec 2016 10:04:41 -0500
parents	05087b27692a
children	5053a18d9bc8

comparison

equal deleted inserted replaced

-:05087b27692a
+:7e6fd3d0f16e
 <expand macro="requirements" />
 <command detect_errors="exit_code"><![CDATA[
 @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( $reference_source.reference_source_selector ) == "history":
 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
 QUIET=true
 VERBOSITY=ERROR
 &&
 #else:
 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
 #end if
 picard
 MergeBamAlignment
 UNMAPPED_BAM="${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":
 #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>
 <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>
 <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" 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" 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>
 <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="4"/>
 </test>
 </tests>
 <help>
 .. class:: infomark
 **Purpose**
 @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@

Mercurial > repos > devteam > picard

comparison picard_MergeBamAlignment.xml @ 13:7e6fd3d0f16e draft