<tool id="small_rna_maps" name="small_rna_maps" version="2.0.0">
  <description></description>
  <requirements>
        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
        <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
        <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
  </requirements>
  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[
      #for $file in $inputs
          samtools index '$file' &&
      #end for
      python '$__tool_directory__'/small_rna_maps.py 
          --inputs 
      #for $file in $inputs
           '$file'
      #end for
          --sample_names
      #for $sample in $inputs
          '$sample.name'
      #end for
      #if str($plots_options.plots_options_selector ) == "two_plot":
          --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
          --outputs '$output_tab' '$extra_output_tab' &&
      #else:
          --plot_methods '${plots_options.first_plot}'
          --outputs '$output_tab' &&
      #end if
      Rscript '$__tool_directory__'/small_rna_maps.r
          --first_dataframe '$output_tab' 
          --extra_dataframe '$extra_output_tab'
          #if str($plots_options.plots_options_selector ) == "two_plot":
              --first_plot_method '${plots_options.first_plot}'
              --extra_plot_method '${plots_options.extra_plot}'
          #else:
              --first_plot_method '${plots_options.first_plot}'
              --extra_plot_method ''
          #end if
          --output_pdf '$output_pdf'
  ]]></command>
 <inputs>
    <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
    <conditional name="plots_options">
        <param name="plots_options_selector" type="select" label="Number of plots per chromosome">
            <option value="one_plot">Just one plot per chromosome</option>
            <option value="two_plot" selected="True">Two plots per chromosome</option>
        </param>
        <when value="two_plot">
            <param name="first_plot" type="select" label="select the type of the first plot">
                <option value="Counts">Counts</option> 
                <option value="Coverage">Coverage</option> 
                <option value="Mean">Mean Sizes</option> 
                <option value="Median">Median Sizes</option>
                <option value="Size">Size Distributions</option>
            </param>
            <param name="extra_plot" type="select" label="select the type of the second plot">
                <option value="Counts">Counts</option> 
                <option value="Coverage">Coverage</option> 
                <option value="Mean">Mean Sizes</option> 
                <option value="Median">Median Sizes</option>
                <option value="Size">Size Distributions</option>
            </param>
        </when>
        <when value="one_plot">
            <param name="first_plot" type="select" label="select the type of the first plot">
                <option value="Counts">Counts</option> 
                <option value="Coverage">Coverage</option> 
                <option value="Mean">Mean Sizes</option> 
                <option value="Median">Median Sizes</option>
                <option value="Size">Size Distributions</option>
            </param>
        </when>
    </conditional>
 </inputs>

 <outputs>
   <data format="tabular" name="output_tab" label="Read Count dataframe" />
   <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
    <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
   </data> 
   <data format="pdf" name="output_pdf" label="PDF file" />

</outputs>

    <tests>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Mean" />
            <output file="count.tab" name="output_tab" />
            <output file="mean.tab" name="extra_output_tab" />
            <output file="count-mean.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Mean" />
            <output file="doubled_count.tab" name="output_tab" />
            <output file="doubled_mean.tab" name="extra_output_tab" />
            <output file="doubled_count-mean.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Median" />
            <output file="count.tab" name="output_tab" />
            <output file="median.tab" name="extra_output_tab" />
            <output file="count-median.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Coverage" />
            <output file="count.tab" name="output_tab" />
            <output file="coverage.tab" name="extra_output_tab" />
            <output file="count-coverage.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Counts" />
            <param name="extra_plot" value="Size" />
            <output file="count.tab" name="output_tab" />
            <output file="size.tab" name="extra_output_tab" />
            <output file="count-size.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="two_plot" />
            <param name="first_plot" value="Size" />
            <param name="extra_plot" value="Counts" />
            <output file="size.tab" name="output_tab" />
            <output file="count.tab" name="extra_output_tab" />
            <output file="size-count.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Counts" />
            <output file="count.tab" name="output_tab" />
            <output file="count.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Size" />
            <output file="size.tab" name="output_tab" />
            <output file="size.pdf" name="output_pdf" />
        </test>
        <test>
            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
            <param name="plots_options_selector" value="one_plot" />
            <param name="first_plot" value="Coverage" />
            <output file="coverage.tab" name="output_tab" />
            <output file="coverage.pdf" name="output_pdf" />
        </test>
    </tests>


<help>

**What it does**

Generate read count maps from alignment BAM files, using pysam and lattice.

In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted.	

**Inputs**

bam alignment files that must be

  - single-read
  - sorted
  - mapping to the same reference

**Output**

A pdf file generated by the R package lattice

One or two dataframes used to plot data

</help>

<citations>
    <citation type="doi">10.1093/bioinformatics/btp352</citation>
     <citation type="bibtex">@Book{,
    title = {Lattice: Multivariate Data Visualization with R},
    author = {Deepayan Sarkar},
    publisher = {Springer},
    address = {New York},
    year = {2008},
    note = {ISBN 978-0-387-75968-5},
    url = {http://lmdvr.r-forge.r-project.org},
  }</citation>
</citations>
</tool>