annotate picard_BedToIntervalList.xml @ 1:5f1da1eadb39 draft default tip

add symlinked macros file

<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="1.135">
  <description>convert coordinate data into picard interval list format</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}" &amp;&amp;
       
    #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
      
      &amp;&amp;
      
    #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 
    
    java -jar \$JAVA_JAR_PATH/picard.jar
      BedToIntervalList
      INPUT="${inputFile}"
      OUTPUT="${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="2" />
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <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>
</tool>