comparison picard_BedToIntervalList.xml @ 13:7e6fd3d0f16e draft

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

12:05087b27692a

    <import>picard_macros.xml</import>
  </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 ) ## 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="${inputFile}"
      OUTPUT="${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>

            <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">

      <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**

13:7e6fd3d0f16e

    <import>picard_macros.xml</import>
  </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 -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 ) ## 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='$inputFile.element_identifier'
      OUTPUT="${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>

            <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">

      <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**