annotate picard_BedToIntervalList.xml @ 33:3f254c5ced1d draft default tip

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

<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>convert coordinate data into picard interval list format</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@
    @symlink_element_identifier@
    #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 ) ## getting path of reference fasta file (must end with .fa)
      #set $picard_dict=$ref_fasta[:-2]+"dict"                        ## replacing .fa with .dict

    #end if

    picard
      BedToIntervalList
      --INPUT '$escaped_element_identifier'
      --OUTPUT '${outFile}'

      --SEQUENCE_DICTIONARY '${picard_dict}'
      --QUIET true
      --VERBOSITY ERROR

  ]]></command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Load picard dictionary file 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="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset"/>
    </inputs>
    <outputs>
        <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
    </data>
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history"/>
            <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta"/>
            <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
            <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format.

@dataset_collections@

@description@

  SEQUENCE_DICTIONARY=File
  SD=File                       The sequence dictionary. You can either use dictionary pre-cached
                                on this instance of Galaxy, or create one on teh fly from a FASTA
                                file uploaded to history (right pane of the interface).


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