<tool name="NPS" id="peakcalling_nps">
    <description>Nucleosome Positioning from Sequencing</description>
    <command interpreter="command">/bin/bash $shscript</command>
    <inputs>
      <param format="bed" name="bfile" type="data" label="BED file(center will be aligned, 35,000,000 lines max)" />
      <param name="use_wavelet" type="boolean" label="use wavelet to denoising?" checked="no" truevalue="yes" falsevalue="no" /> 

      <conditional name="pre">
        <param name="pre_select" type="select" label="------- Preprocessing Options -------">
          <option value="no">Use defaults</option>
          <option value="yes">Show settings</option>
        </param>
        <when value="yes">
          <param name="fragment_size" type="integer" label="The estimate fragment size (bp)" value="150">
            <validator type="in_range" max="400" min="75" message="Extension shoube in range 75 - 400" />
          </param>
          <param name="sort" type="boolean" label="sort the tags?" checked="yes" truevalue="yes" falsevalue="no"/>
          <param name="tag_thread" type="integer" label="minimum tag count to declare as a peak" value="2" />
        </when>
        <when value="no">
          <param name="fragment_size" type="hidden" value="150"/>
          <param name="sort" type="hidden" value="yes"/>
          <param name="tag_thread" type="hidden" value="2"/>
        </when>
      </conditional>

      <conditional name="wavelet">
        <param name="wavelet_select" type="select" label="------- Wavelet Denoising Options (Better use default.) -------">
          <option value="no">Use defaults</option>
          <option value="yes">Show settings</option>
        </param>
        <when value="yes">
          <param name="wav_decomp_level" type="integer" label="which level of wavelet decomposition" value="2" />
          <param name="wav_method" type="select" label="use what kind of wavelet denosing?">
            <option value="coif4">coif4</option>
          </param>
          <param name="wav_threshold_est" type="select" label="Use what for denoising threshold selection?">
            <option value="heursure">heursure</option>
          </param>
          <param name="wav_threshold_type" type="select" label="type of threshold?">
            <option value="soft">soft</option>
          </param>
          <param name="wav_scale" type="text" label="scale of denosing" value="mln" />
        </when>
        <when value="no">
          <param name="wav_decomp_level" type="hidden" value="2"/>
          <param name="wav_method" type="hidden" value="coif4"/>
          <param name="wav_threshold_est" type="hidden" value="heursure"/>
          <param name="wav_threshold_type" type="hidden" value="soft"/>
          <param name="wav_scale" type="hidden" value="mln"/>
        </when>
      </conditional>

      <conditional name="peakfind">
        <param name="peakfind_select" type="select" label="------- Peak Finding Options -------">
          <option value="no">Use defaults</option>
          <option value="yes">Show settings</option>
        </param>
        <when value="yes">
          <param name="peakf_pvalue" type="text" label="p value cut-off for identifying nucleosomes" value="1e-5" />
          <param name="peakf_min_w" type="integer" label="minimum peak width" value="80" />
          <param name="peakf_max_w" type="integer" label="maximum peak width" value="250" />
          <param name="peakf_PIR" type="text" label="minimum peak to inflection point ratio" value="1.2" />
          <param name="peakf_bios_ratio" type="float" label="allowable ratio between + tags and – tags" value="4" />
        </when>
        <when value="no">
          <param name="peakf_pvalue" type="hidden" value="1e-5"/>
          <param name="peakf_min_w" type="hidden" value="80"/>
          <param name="peakf_max_w" type="hidden" value="250"/>
          <param name="peakf_PIR" type="hidden" value="1.2"/>
          <param name="peakf_bios_ratio" type="hidden" value="4"/>
        </when>
      </conditional>
    </inputs>
    <outputs>
      <data format="bed" name="outputbed" label="NPS peak output for ${bfile.name}" />
      <data format="wig" name="outputwig" label="NPS wig output for ${bfile.name}" />
      <data format="txt" name="log" label="NPS log" />
      <data format="txt" name="tagfile" label="NPS tag file" />
    </outputs>
    <configfiles>
      <configfile name="tag_file">
#import sys
#import os

#set $dollar = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)

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

#if $bfile.metadata.dbkey == "hg18"
#set $genome_len = str(2770000000)
#end if
#if $bfile.metadata.dbkey == "hg19"
#set $genome_len = str(2790000000)
#end if
#if $bfile.metadata.dbkey == "mm8"
#set $genome_len = str(1870000000)
#end if
#if $bfile.metadata.dbkey == "mm9"
#set $genome_len = str(1910000000)
#end if
#if $bfile.metadata.dbkey == "ce4"
#set $genome_len = str(90300000)
#end if
#if $bfile.metadata.dbkey == "ce6"
#set $genome_len = str(90300000)
#end if
#if $bfile.metadata.dbkey == "dm2"
#set $genome_len = str(119000000)
#end if
#if $bfile.metadata.dbkey == "dm3"
#set $genome_len = str(152000000)
#end if


#set $shiftsize = (int($pre.fragment_size.value)-75)/2

\# Parameters for ChIP Sequence data analysis.


\# Input and output files

INFILE = $bfile
OUTFILE = $outputbed
OUTFILEWIG = $outputwig

\# Preprocessing

SPENAME = $bfile.metadata.dbkey
EXTENSION = 75
SHIFT = $shiftsize
WANT_SORT = $pre.sort
TAG_THR = $pre.tag_thread

\# Wavelet denoising

WANT_DENOISE = $use_wavelet
DECOMP_LEVEL = $wavelet.wav_decomp_level
WAVELET = $wavelet.wav_method
THRESHOLD_EST = $wavelet.wav_threshold_est
THRESHOLD_TYPE = $wavelet.wav_threshold_type
SCALE = $wavelet.wav_scale

\# Peak finding

INTERVAL = 10
GENOME_LEN = $genome_len
PVALUE = $peakfind.peakf_pvalue
TAG_NUM = NEED_TO_FILE_IN_LATER
LOG = 3
SLOPE = 2
MIN_WIDTH = $peakfind.peakf_min_w
MAX_WIDTH = $peakfind.peakf_max_w
MIN_HEIGHT = 0
MAX_HEIGHT = 10000
PEAK_INFLECTION_RATIO = $peakfind.peakf_PIR
MED_WSIZE = 5
BIAS_RATIO = $peakfind.peakf_bios_ratio

      </configfile>
      <configfile name="shscript">
#set $gt = chr(62)
#set $ad = chr(38)
#set $dollar = chr(36)

tagnum=`grep -c -v ^\# $bfile`
perl -pi -e s/NEED_TO_FILE_IN_LATER/${dollar}tagnum/ $tag_file
if [[ ${dollar}tagnum -gt 35000000 ]];then
    echo "bed file is too big! 35M lines is the maximum!" ${gt}${ad} $log
    exit;
fi

SeqTag.py $tag_file ${ad}${gt} $log
cp $tag_file $tagfile
      </configfile>
    </configfiles>
    <help>
NPS

Please find instruction and parameters here.
http://liulab.dfci.harvard.edu/NPS/

.. class:: warningmark

**NEED IMPROVEMENT**

-----

**Outputs**

- **BED file** for nucleosome locations in BED format
- **LOG file** job log. If you see errors, please attach this in
  the bug report
- **TAG file** with all the information input into the tool

    </help>
</tool>