Mercurial > repos > devteam > picard
diff picard_MergeBamAlignment.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_MergeBamAlignment.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MergeBamAlignment.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,22 +1,24 @@ -<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ +<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <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}" "${ref_fasta}" && + ln -sf '${reference_source.ref_file}' '${ref_fasta}' && #if str( $reference_source.reference_source_selector ) == "history": - picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" - QUIET=true - VERBOSITY=ERROR + picard CreateSequenceDictionary + -REFERENCE '${ref_fasta}' + -OUTPUT '${picard_dict}' + -QUIET true + -VERBOSITY ERROR && @@ -26,181 +28,166 @@ #end if - picard - MergeBamAlignment - UNMAPPED_BAM="${unmapped_bam}" + picard MergeBamAlignment + --UNMAPPED_BAM '${unmapped_bam}' - PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false} + --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}" + --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}" + --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}" + --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}" + --READ1_ALIGNED_BAM '${dataset.read1_aligned_bam}' #end for #end if - OUTPUT="${outFile}" - REFERENCE_SEQUENCE="${ref_fasta}" + --OUTPUT '${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="${max_insertions_or_deletions}" + --CLIP_ADAPTERS '${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 $attributes_to_retain: - ATTRIBUTES_TO_RETAIN="${$attribute.attribute}" + --ATTRIBUTES_TO_RETAIN '${$attribute.attribute}' #end for #for $attribute in $attributes_to_remove: - ATTRIBUTES_TO_REMOVE="${$attribute.attribute}" + --ATTRIBUTES_TO_REMOVE '${$attribute.attribute}' #end for - READ1_TRIM="${read1_trim}" - READ2_TRIM="${read2_trim}" + --READ1_TRIM '${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}" + --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}" + --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}" + --VALIDATION_STRINGENCY '${validation_stringency}' - SORT_ORDER=coordinate - QUIET=true - VERBOSITY=ERROR + --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"/> + <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" 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> - </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> - <outputs> - <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM"/> - </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="orientations" 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="4"/> - </test> - </tests> - - - <help> + <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> + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM"/> + </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="orientations" 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="4"/> + </test> + </tests> + <help> .. class:: infomark @@ -309,5 +296,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>