<tool name="Conservation Plot" id="ceas_conservation">
  <description>Calculates the PhastCons scores in several intervals sets</description>
  <command interpreter="command">/bin/bash $shscript</command>
  <inputs>

    <repeat name="more" title="interval file">
      <param ftype="interval" format="bed,interval" name="bfile" type="data" label="Select another interval file(100,000 lines max)"/>
      <param name="blabel" type="text" label="BED file label"
      help="label on the figure" optional="false"/>
    </repeat>

    <param name="size" type="integer" label="window size around the center" value="3000">
    	<validator type="in_range" max="10000" min="100" message="window size is out of range, window size has to be between 100 to 10000" />
    </param>
    <param name="gv" type="select" label="UCSC genome/assembly version">
      <option value="hg38">hg38</option>
      <option value="hg19/placentalMammals">hg19 (placental mammals)</option>
      <option value="hg19/vertebrate">hg19 (vertebrate)</option>
      <option value="hg18/placentalMammals">hg18 (placental mammals)</option>
      <option value="hg18/vertebrate">hg18 (vertebrate)</option>
      <option value="mm10/placental">mm10 (placental)</option>
      <option value="mm9/placental">mm9 (placental)</option>
      <option value="mm9/vertebrate">mm9 (vertebrate)</option>
      <option value="mm8/vertebrate">mm8 (vertebrate)</option>
      <option value="dm3">dm3</option>
      <option value="danRer7">danRer7 (vertebrate)</option>
      <option value="ce10">ce10</option>
      <option value="ce6">ce6</option>
      <option value="ce4">ce4</option>
    </param>
    <param type="select" name="imagetype" display="radio" label="Image Type">
      <option value="PDF">PDF format</option>
      <option value="PNG">PNG format</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="output">
      <change_format>
	<when input="imagetype" value="PDF" format="pdf" />
      </change_format>
    </data>
    <data format="txt" name="outputr" label="conservation R script" />
    <data format="txt" name="log" label="conservation job log"/>
  </outputs>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash
#import os

#set $dollar = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)
#set $tmp = ""
#set $bedcount = 0

#set $path = $os.path.abspath($__app__.config.tool_path)

#for $m in $more
#set $bedcount = $bedcount + 1 
   lines=`wc -l $m.bfile | tail -1 | awk '{print ${dollar}1}'`
   format=`$path/validation/fcfunc.py $m.bfile`
   if [[ ${dollar}lines -gt 100000 ]];then
      echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2
      exit;
   fi
   if [[ ${dollar}format != "passed" ]]; then
      echo "Bed file ${bedcount}: "${dollar}format ${gt}${ad}2
      exit;
   fi
   
   bedlabel=`echo $m.blabel |awk '{print length(${dollar}0)}'`
   if [[ ${dollar}bedlabel -gt 255 ]];then
       echo "Bed Label exceed the limit of 255 characters!" ${gt}${ad}2;
       exit;
   fi
   if [[ ${dollar}bedlabel -eq 0 ]];then
       echo "Bed Label is required!" ${gt}${ad}2;
       exit;
   fi
#set $tmp = $tmp + str($m.bfile) + " -l '" + str($m.blabel) + "' "
#end for

if [[ $bedcount -eq 0 ]];then
    echo "Need at least one bed file" ${gt}${ad}2
    exit;
fi

#set $datapath = os.path.join( os.path.abspath($__app__.config.cistrome_static_library_path), "conservation", $gv.value )

conservation_plot.py -d $datapath -w $size $tmp ${ad}${gt} $log

if [ $imagetype.value == "PNG" ]; then
convert tmp.pdf tmp.png
mv tmp.png $output
else
mv tmp.pdf $output
fi
mv tmp.R $outputr

    </configfile>
  </configfiles>
<tests>
  <test maxseconds="3600" name="Conservation_1">
    <param name="bfile" value="bedfile.bed" />
    <param name="blabel" value="conservation_1" />
    <param name="size" value="1000" />
    <param name="gv" value="ce6" />
    <output name="output" file="conservation_1/conservation_1.bmp" />
    <output name="output" file="conservation_1/conservation_1.log" lines_diff = "200" />
  </test>
</tests>
  <help>
This tool plots the PhastCons scores prfiles in several BED
files. It's based on conservation_plot.py script in Tao Liu's
library. Original code is written by Ying Lei, then modified by
Jaqueline Wentz.

.. class:: infomark

**Tip:** If you see red Xs, check the BED input file first. Perhaps, the BED file contains some abnormal chromosome names.  

.. class:: infomark

**Tip:** For best performance, please make sure the regions in the BED file are centered at peak summits.

-----

**Parameters**

- **Title** Conservation Plot Tool
- **Interval file** is a BED file normally centered at peak summit. 
- **BED file label** is the label marked in the legend of the final figure.
- **more** You can add more BED files and labels.
- **Window size** is the regions around peak centers to extract PhastCons scores.
- **UCSC genome version** must be selected according to your BED files.

-----

**script parameter list for conservation_plot.py**

conservation_plot.py

Draw conservation plot for many bed files.

Options:
  --version             show program's version number and exit
  -H HEIGHT, --height=HEIGHT
                        height of plot
  -W WIDTH, --width=WIDTH
                        width of plot
  -w W                  window width centered at middle of bed
                        regions,default: 1000
  -t TITLE, --title=TITLE
                        title of the figure. Default: 'Average Phastcons
                        around the Center of Sites'
  -d PHASDB, --phasdb=PHASDB
                        The directory to store phastcons scores in the server
  -l BEDLABEL, --bed-label=BEDLABEL
                        the BED file labels in the figure. No space is
                        allowed. This option should be used same times as -w
                        option, and please input them in the same order as BED
                        files. default: will use the BED file filename as
                        labels.
  -h, --help            Show this help message and exit.


  </help>

</tool>