<tool id="Stampy" name="Stampy" version="1.0.21">
    <description>is a package for mapping of short reads from illumina sequencing machines onto a reference genome</description>
     <command interpreter="python">  stampy_wrapper.py 

      ## Indexing of the reference genome
      --assembly=$Assembly 
      --species=$species
      --genome_index=$G 
      --output=$output

      ## Reference genome for creating index
      --genome=$input
      #if $refGenomeSource.genomeSource == "indexed":
      --genome1="${refGenomeSource.index.fields.path}"
      #end if
      ## input file for single paired read
          --input1=$input1
        
        ## Second input only if input is paired-end.
        #if $singlePaired.sPaired == "paired"
            --input1=$singlePaired.input1 
            --input2=$singlePaired.input2
        #end if
     ## Parameters
      --settings=$params.settingsType
   	#if $params.settingsType == "full":
        --sd=${params.d}
   	--insert=${params.i}
   	--subrate=${params.r}
       	#end if  
     </command>
    <inputs>
        <param name="Assembly" type="text" value=""/>
	<param name="species" type="text" value=""/>
        <param name="G" type="text" value=""/>

       <conditional name="refGenomeSource">
          <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
            <option value="indexed">Use a built-in index</option>
            <option value="history" selected="true">Use one from the history</option>
          </param>
          <when value="indexed">
             <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
              <options from_file="stampy_indices.loc">
                 <column name ="value" index="0" />
                 <column name ="name" index="1" />
              </options>
        </param>
          </when>
          <when value="history">hg18_
            <param name="input" type="data" format="fna" metadata_name="dbkey" label="Select the reference genome" />
          </when> 
        
        </conditional>  
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library mate-paired?">
              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param format="fna" name="input1" type="data" label="Input sequence" />
            </when>
            <when value="paired">
                <param format="fna" name="input1" type="data" label="Input sequence"  />
                <param format="fna" name="input2" type="data" label="Input sequence"  />
            </when>
        </conditional>
        <conditional name="params">
            <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
              <option value="preSet">Use Defaults</option>
              <option value="full">Full parameter list</option>
            </param>
            <when value="preSet" />
            <!-- Full/advanced parameters. -->
            <when value="full">
        <param name="i" type="text" value="250" label="Insert size" />
        <param name="d" type="text" value="50" label="standard deviation" />
        <param name="r" type="text" value="0.001" label="substitutionrate" />
 	</when>  <!-- full -->
      </conditional>  <!-- params -->

    </inputs>

<outputs>
    <data format="txt" name="output" label="outfile"/>
</outputs>
<help>
**Stampy**

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome (http://www.well.ox.ac.uk/project-stampy). Selected options used here are given below

------

**Indexing usage**

*Building index*

stampy.py --species=human --assembly=hg18_ncbi36 -G hg18 /data/genomes/hg18/*.fa.gz

*Building hash*

stampy.py -g hg18 -H hg18

------


**Alignment usage**

 stampy.py options -g hg18 -h hg18 -M reads_1.fastq reads_2.fastq


------

**Options - Description**

--insertsize

Set the mean insert size for paired-end reads (default: 250)

--insertsd=N                 

Set the standard deviation of the insert size distribution (default: 60)

--substitutionrate=S		 

 Introduce an expected fraction S of Poisson-distributed substitutions  (default: 0.001)


</help>

</tool>