<tool id="tapdance_runner" name="TAPDANCE" version="1.0" force_history_refresh="True">
  <description>A tool for identifying Common Insertion Sites</description>
  <command interpreter="perl">tapdance_runner.pl -index $index -index_id $index.id -index_path $index.extra_files_path
    #if $predef.predef_select.__str__() == 'PREDEF':
      -s $predef.seqs -b $predef.bar2lib -pn $userEmail$predef.proj_name -config $predef.config
    #else
      ## INPUT
      #if $predef.start_point.start_select.__str__() == 'sequences':
        -s $predef.start_point.seqs -b $predef.start_point.bar2lib -bowtieIdx $predef.start_point.genomeIdx -pn $userEmail$predef.start_point.proj_name 
        #for $entry in $predef.start_point.mutagens
          #if $entry.mutagen.mutagen_select.__str__() == 'CUSTOM':
            -mutagen $entry.mutagen.mutagen_custom.__str__()
          #else
            -mutagen $entry.mutagen.mutagen_select.__str__()
          #end if
        #end for
      #end if
      #if $predef.start_point.start_select.__str__() == 'single_project':
        -pn $predef.start_point.cis_project.__str__()
      #end if
      #if $predef.start_point.start_select.__str__() == 'multiple_projects':
        -pn $userEmail$predef.start_point.proj_name -merge $predef.start_point.merge_projects.__str__() 
      #end if

      ## OUTPUT
      #if $predef.start_point.start_select.__str__() != 'single_project':
        -pb $projBed -projectBedId $projBed.id 
        ##-ps $projSum -projectSummaryId $projSum.id -pv $projVis -projectVisId $projVis.id 
      #end if
      #if $predef.results.result_select.__str__() == 'cis':
        -cw $cisWig -cwid $cisWig.id -cwpath $__new_file_path__ 
        ##-cs $cisSum -cisSumId $cisSum.id 
        -lib_pct $predef.results.cis_params.lib_pct -CIS_tot_p $predef.results.cis_params.CIS_tot_p -CIS_lib_p $predef.results.cis_params.CIS_lib_p -CIS_reg_p $predef.results.cis_params.CIS_reg_p -coCIS_thresh $predef.results.cis_params.coCIS_thresh 
        #if $predef.results.metadata.metadata_select.__str__() == 'CUSTOM':
          -m $predef.results.metadata.metadata_custom.__str__()
        #end if
        #if $predef.results.annotation.annotation_select.__str__() == 'CUSTOM':
          -m $predef.results.annotation.annotation_file.__str__()
        #end if
        #for $entry in $predef.results.omitChroms
          -o $entry.omitChrom.__str__()
        #end for
      #else
        -no_cis
      #end if
    #end if
  </command>
  <inputs>
    <conditional name="predef">
      <param name="predef_select" type="select" label="Enter values below or use a predefined config file?">
	<option value="CUSTOM">Enter values below</option>
	<option value="PREDEF">Use predefined config file</option>
      </param>
      <when value="PREDEF">
	<param name="proj_name" type="text" label="New Project Name" optional="false"/>
        <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/>
        <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/>
	<param name="config" type="data" format="text" label="Predefined Config File" optional="false"/>
	<conditional name="metadata">
          <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom">
	    <option value="AUTOMATIC">Generate default</option>
	    <option value="CUSTOM">Use uploaded data</option>
          </param>
          <when value="AUTOMATIC">
	    <param name="metadata_custom" type="hidden" value=""/>
          </when>
          <when value="CUSTOM">
	    <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/>
          </when>
        </conditional>
      </when>
      <when value="CUSTOM">
	<conditional name="start_point">
	  <param name="start_select" type="select" label="Starting Point">
	    <option value="sequences">FASTQ or FASTA</option>
	    <option value="single_project">Existing Project</option>
	    <option value="multiple_projects">Merge Multiple Projects</option>
	  </param>
	  <when value="sequences">
	    <param name="proj_name" type="text" label="New Project Name" optional="false"/>
            <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/>
            <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/>
            <repeat name="mutagens" title="Mutagen(s)" min="1">
              <conditional name="mutagen">
		<param name="mutagen_select" type="select" label="Mutagen matching" help="Choose the appropriate match for this experiment">
		  <option value="TGTATGTAAACTTCCGACTTCAACTG">Sleeping Beauty Example, TGTATGTAAACTTCCGACTTCAACTG</option>
		  <option value="CUSTOM">Other</option>
		</param>
		<when value="TGTATGTAAACTTCCGACTTCAACTG">
		  <param name="mutagen_custom" type="hidden" value=""/>
		</when>
		<when value="CUSTOM">
		  <param name="mutagen_custom" type="text" label="Mutagen Sequence" help="Enter the sequence to match as the mutagen, '_' may be used to match any single base.  E.G. _GTATGTAAACTTCCGACTTCAACTG would match both AGTATGTAAACTTCCGACTTCAACTG and TGTATGTAAACTTCCGACTTCAACTG"/>
		</when>
              </conditional>
            </repeat>
            <param name="genomeIdx" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact help@msi.umn.edu">
              <options from_file="bowtie_indices.loc">
		<column name="value" index="3" />
		<column name="name" index="0" />
              </options>
            </param>
	  </when>
	  <when value="single_project">
	    <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/>
            <param name="cis_project" type="select" label="Project" data_ref="proj_source">
              <options from_dataset="proj_source">
		<column name="name" index="1"/>
		<column name="value" index="0"/>
              </options>
            </param>
	  </when>
	  <when value="multiple_projects">
	    <param name="proj_name" type="text" label="New Project Name" optional="false"/>
            <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/>
            <param name="merge_projects" type="select" multiple="true" label="Projects to Merge" data_ref="proj_source">
              <options from_dataset="proj_source">
		<column name="name" index="1"/>
		<column name="value" index="0"/>
              </options>
            </param>
	  </when>
	</conditional>
	<conditional name="results">
	  <param name="result_select" type="select" label="Desired Results">
	    <option value="cis">CIS calls</option>
	    <option value="inserts">Inserts Only (useful for QC)</option>
	  </param>
	  <when value="inserts">
	    <param type="hidden" value="" name="inserts_only"/>
	  </when>
	  <when value="cis">
	    <conditional name="metadata">
              <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom">
		<option value="AUTOMATIC">Generate default</option>
		<option value="CUSTOM">Use uploaded data</option>
              </param>
              <when value="AUTOMATIC">
		<param name="metadata_custom" type="hidden" value=""/>
              </when>
              <when value="CUSTOM">
		<param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/>
              </when>
            </conditional>
	    <repeat name="omitChroms" title="Chromosomes to Omit" help="The chromosome of the donor concatemer is often omitted">
              <param type="text" name="omitChrom" label="Chromosome Label" help="e.g. chr1"/>
            </repeat>
	    <conditional name="annotation">
	      <param name="annotation_select" label="Annotation Features" type="select" help="Specify an interval file containing genomic features to annotate CIS calls">
		<option value="DEFAULT">Default: mm9 refSeq genes</option>
		<option value="CUSTOM">Specify interval file</option>
	      </param>
	      <when value="DEFAULT">
		<param type="hidden" name="annotation_file" value=""/>
	      </when>
	      <when value="CUSTOM">
		<param type="data" format="interval" name="annotation_file" label="Annotation Source"/>
	      </when>
	    </conditional>
	    <conditional name="cis_params">
              <param name="cis_params_select" type="select" label="CIS calling parameters">
		<option value="default">Use defaults</option>
		<option value="custom">Specify values</option>
              </param>
              <when value="default">
		<param type="hidden" value="0.0001" name="lib_pct"/>
		<param type="hidden" value="0.05" name="CIS_tot_p"/>
		<param type="hidden" value="0.05" name="CIS_lib_p"/>
		<param type="hidden" value="0.05" name="CIS_reg_p"/>
		<param type="hidden" value="0.0001" name="coCIS_thresh"/>
              </when>
              <when value="custom">
		<param type="float" value="0.0001" name="lib_pct" label="Library Percent"/>
		<param type="float" value="0.05" name="CIS_tot_p" label="CIS Total pvalue"/>
		<param type="float" value="0.05" name="CIS_lib_p" label="CIS Library pvalue"/>
		<param type="float" value="0.05" name="CIS_reg_p" label="CIS Region pvalue"/>
		<param type="float" value="0.0001" name="coCIS_thresh" label="coCIS Threshold"/>
              </when>
            </conditional>
	  </when>
	</conditional>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="html" name="index" label="TAPDANCE Results"/>
    <data format="bed" name="projBed" label="Non Redundant Inserts BED" visible="false">
      <filter>(
	predef['predef_select'] == 'PREDEF' or
	predef['start_point']['start_select'] != 'single_project'
	)
      </filter>
    </data>
    <!--
    <data format="txt" name="projSum" label="Summary" hidden="true">
      <filter>(
	predef['predef_select'] == 'PREDEF' or 
	predef['start_point']['start_select'] == 'sequences'
	)
      </filter>
    </data>
   <data format="pdf" name="projVis" label="Insert Graphs">
	<filter>(predef['predef_select'] == 'PREDEF' or predef['start_point']['start_select'] != 'single_project')</filter>
    </data>
   -->
    <!-- due to optional start with seqs, can no longer use the seqs metadata as a source for cisWig metadata -->
    <data format="wig" name="cisWig" label="CIS WIG">
      <filter>(
	predef['predef_select'] == 'PREDEF' or
	predef['results']['result_select'] == 'cis'
	)
      </filter>
    </data>
    <!--
    <data format="txt" name="cisSum" label="CIS Summary">
      <filter>(
	predef['predef_select'] == 'PREDEF' or 
	predef['results']['result_select'] == 'cis'
	)
      </filter>
    </data>
    -->  
  </outputs>
  <!--<code file="tapdance_index.py">
    <hook exec_after_process="exec_after_completion" />
  </code>-->
  <help>
    See full help at https://sourceforge.net/p/tapdancebio/wiki/
    
    `Report a Problem`_

    .. _Report a Problem: https://sourceforge.net/p/tapdancebio/tickets/new/

  </help>
</tool>