<tool id="snvmix" name="SNVMix" version="0.12.1-rc1">
  <requirements>
    <requirement type="package">SNVMix</requirement>
  </requirements>
  <description>performs SNV calling on a bam file</description>
  <command interpreter="python">
    snvmix.py
      -i $input1
      -d ${input1.metadata.dbkey}
      -o $output_snvmix
      -t $type
      #if $positionFile == "yes":
        -l $pos
      #else:
        -l 'none'
      #end if
      -x ${GALAXY_DATA_INDEX_DIR}
      -q $q
      -Q $Q
      -f $full
      -R $keep_dups
      -c $keep_chastity
  </command>
 <inputs>
   <param name="type" type="select" label="model used">
     <option value="MB">Filter on map quality AND base quality (MB)</option>
     <option value="SNVMix1">SNVMix1</option>
     <option value="mb">Lowest between map and base quality is used (mb)</option>
     <option value="m">Filter on map quality and use as a surrogate for base quality (m)</option>
     <option value="b">Filter on base quality and set map quality to 1 (b)</option>
     <option value="Mb">Filter on map quality and use both map and base qualities (Mb)</option>
    </param> 
    <conditional name="refOrHistory">
      <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
        </param>
      </when>
      <when value="history">
        <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" />
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
      </when>
    </conditional>
    <param name="q" type="integer" value="19" label="Cutoff Phred value for Base Quality, anything less than or equal to this value is ignored" />
    <param name="Q" type="integer" value="19" label="Cutoff Phred value for Map Quality, anything less than or equal to this value is ignored" />
    <conditional name="positionFile">
      <param name="positions" type="select" label="Will you provide a set of positions for SNV calling?">
	<option value="no">No, call variants at every position</option>
        <option value="yes">Yes, select one from the history</option>
      </param>
      <when value="yes">
        <param name="pos" type="data" format="tabular" label="select the tab-delimited file containing positions">
        </param>
      </when>
    </conditional>
    <param name="full" type="select" label="Do you want SNVMix to calculate probabilities for each of these positions? (only works in conjunction with above option)">
      <option value="no">No, I just want possible variants output</option>
      <option value="yes">Yes (I know this could generate a huge file)</option>
    </param>
    <param name="keep_dups" type="select" label="Do you want SNVMix to include reads flagged as duplicates? (only works if Picard or some other tool has set this bit in your bam file">
      <option value="no">No (ignore duplicates for variant calling)</option>
      <option value="yes">Yes (use all reads)</option>
    </param>
    <param name="keep_chastity" type="select" label="Do you want SNVMix to include reads flagged as failing the chastity filter? (only works if Picard or some other tool has set this bit in your bam file">
      <option value="no">No (ignore filtered reads for variant calling)</option>
      <option value="yes">Yes (use all reads)</option>
    </param>
</inputs>

  <outputs>
    <data format="tabular" name="output_snvmix" label="${tool.name}: Raw SNVMix calls" />
  </outputs>
  <help>

**What it does**

This tool uses the SNVMix model (Goya et al) to call single nucleotide variants (SNVs) from a bam file.  The various models described in the study are provided (e.g. SNVMix1, MB, Mb etc.).  The most commonly-used models are MB (the default) and SNVMix1.  The former thresholds on base quality and mapping quality and uses both qualities in the variant prediction while the latter filters on both and only uses the allele counts in the model.  The output is a tab-delimited file that should be passed through the accompanying filtering script prior to use.  

  </help>
</tool>