comparison picard_MergeBamAlignment.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

32:f9242e01365a

<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[
    @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":
        #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" 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>

.. class:: infomark

**Purpose**

@more_info@
  </help>
  <expand macro="citations" />
</tool>

33:3f254c5ced1d

<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 -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

      &&

    #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":
        #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" 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>

.. class:: infomark

**Purpose**

@more_info@
  </help>
    <expand macro="citations"/>
</tool>