<tool name="SitePro: Aggregation plot tool for signal profiling" id="ceas_sitepro">
  <description>Draw the score profile near a given interval</description>
  <command interpreter="command">/bin/bash $shscript</command>
  <inputs>
    <conditional name="mode">
      <param name="mode_select" type="select" label="Sitepro behaviour mode" force_select="true">
	<option value="single"> 1 wiggle / bigwig vs 1 BED file</option>
	<option value="multiwig"> multiple wiggle / bigwig vs 1 BED</option>
	<option value="multibed"> multiple BED vs 1 wiggle / bigwig</option>
      </param>

      <when value="single">
	<param ftype="wig" format="wig,bigwig" name="wfile" type="data" label="Wiggle / bigwig file"/>
	<param ftype="bed" format="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/>
      </when>

      <when value="multiwig">
	<param format="wig,bigwig" name="wfile" type="data" label="Wiggle / bigwig file"/>
	<param name="label" type="text" label="Wiggle label" optional="false" />
	<repeat name="more" title="wiggle / bigwig file">
	  <param format="wig,bigwig" name="wig" type="data" label="Select another wiggle / bigwig file"/>
	  <param name="label" type="text" label="Wiggle label"  optional="false" />
	</repeat>
	<param format="bed" name="bfile" type="data"
	label="BED file"/>
      </when>

      <when value="multibed">
	<param format="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/>
	<param name="label" type="text" label="BED label" optional="false" />
	<repeat name="more" title="BED file">
	  <param format="bed" name="bfile" type="data" label="Select another BED file(100,000 lines max)"/>
	  <param name="label" type="text" label="BED label"  optional="false" />
	</repeat>
	<param format="wig,bigwig" name="wfile" type="data" label="Wiggle / bigwig file"/>
      </when>

    </conditional>

    <param name="span" type="integer" label="Span" value="1000">
    	<validator type="in_range" max="1000000" min="100" message="Span is out of range, Span has to be between 100 to 1000000" />
    </param>	
    <param name="pfres" type="integer" label="Profiling Resolution" value="50">
    	<validator type="in_range" max="1000" min="10" message="Profiling Resolution is out of range, Profiling Resolution has to be between 10 to 1000" />
    </param>	
    <param name="dir" type="boolean" label="consider the direction (+/-) while profiling" checked="no" truevalue="--dir" falsevalue=" " />
  </inputs>
  <outputs>
    <data format="pdf" name="output" />
    <data format="txt" name="log" label="sitepro job log" />
    <data format="txt" name="dump" label="txt file with profiles" />
  </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 $path = $os.path.abspath($__app__.config.tool_path)

##REMOVING WIG VALIDATORS
##note: validator for wig file size
##if [ $mode.wfile != "None" ];then
##    wfilesize=`du -b $mode.wfile | awk '{print ${dollar}1}'`
##    
##    if [[ ${dollar}wfilesize -gt 2097152000 ]];then
##        echo "wfile file is too big! 2GB is the maximum!" ${gt}${ad}2
##        exit;
##    fi
##fi

##note: validator for wig label
#if $mode.mode_select == "multiwig"
    wiglabel=`echo $mode.label |awk '{print length(${dollar}0)}'`
    if [[ ${dollar}wiglabel -gt 255 ]];then
        echo "Wig Label exceed the limit of 255 characters!" ${gt}${ad}2;
        exit;
    fi
    if [[ ${dollar}wiglabel -eq 0 ]];then
        echo "Wig Label is required!" ${gt}${ad}2;
        exit;
    fi
#end if

##note: validator for bed label
#if $mode.mode_select == "multibed"
    bedlabel=`echo $mode.label |awk '{print length(${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
#end if

lines=`wc -l $mode.bfile | tail -1 | awk '{print ${dollar}1}'`
format=`$path/validation/fcfunc.py $mode.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 1: " ${dollar}format ${gt}${ad}2
   exit;
fi

#if $mode.wfile.extension == "wig"
#set $sitepro = "sitepro"
#elif $mode.wfile.extension == "bigwig"
#set $sitepro = "siteproBW"
#end if

#if $mode.mode_select == "single"
##NOTE: cease, gca, and sitepro require python2.5 and above
$sitepro -w $mode.wfile -b $mode.bfile --span=$span --pf-res=$pfres $dir --name=sitepro_out --dump ${ad}${gt} $log
R --vanilla $lt sitepro_out.R ${ad}${gt}/dev/null
mv sitepro_out.pdf $output
cat *_dump.txt > $dump

#elif $mode.mode_select == "multiwig"
#set $tmp = ""
#for $m in $mode.more
#set $tmp = $tmp + "-w " +str($m.wig) + " -l " + str($m.label)+ " "
#end for
##NOTE: cease, gca, and sitepro require python2.5 and above

$sitepro -w $mode.wfile -l $mode.label $tmp -b $mode.bfile --span=$span --pf-res=$pfres $dir --name=sitepro_out --dump ${ad}${gt} $log
R --vanilla $lt sitepro_out.R ${ad}${gt}/dev/null
mv sitepro_out.pdf $output
cat *_dump.txt > $dump

#elif $mode.mode_select == "multibed"
#set $bedcount = 1
#set $tmp = ""
#for $m in $mode.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
#set $tmp = $tmp + "-b " +str($m.bfile) + " -l " + str($m.label)+ " "
#end for
##NOTE: cease, gca, and sitepro require python2.5 and above
 

$sitepro -w $mode.wfile -b $mode.bfile -l $mode.label $tmp --span=$span --pf-res=$pfres $dir --name=sitepro_out --dump ${ad}${gt} $log
R --vanilla $lt sitepro_out.R ${ad}${gt}/dev/null
mv sitepro_out.pdf $output
cat *_dump.txt > $dump
#end if
    </configfile>
  </configfiles>
<tests>
  <test maxseconds="3600" name="Sitepro_1">
    <param name="mode_select" value="single" />
    <param name="wfile" value="wiggle.wig" />
    <param name="bfile" value="bedfile.bed" />
    <param name="span" value="1000" />
    <param name="pfres" value="50" />
    <output name="output" file="sitepro_1/sitepro_1.pdf" />
    <output name="output" file="sitepro_1/sitepro_1.log" lines_diff = "200" />
    <output name="output" file="sitepro_1/sitepro_1_dump.txt" />
  </test>
  <test maxseconds="3600" name="Sitepro_2">
    <param name="mode_select" value="single" />
    <param name="wfile" value="wiggle.wig" />
    <param name="bfile" value="bedfile.bed" />
    <param name="span" value="1000" />
    <param name="pfres" value="50" />
    <output name="output" file="sitepro_2/sitepro_2.pdf" />
    <output name="output" file="sitepro_2/sitepro_2.log" lines_diff = "200" />
    <output name="output" file="sitepro_2/sitepro_2_dump.txt" />
  </test>
  <test maxseconds="3600" name="Sitepro_3">
    <param name="mode_select" value="single" />
    <param name="wfile" value="wiggle.wig" />
    <param name="bfile" value="bedfile.bed" />
    <param name="span" value="100" />
    <param name="pfres" value="10" />
    <output name="output" file="sitepro_3/sitepro_3.pdf" />
    <output name="output" file="sitepro_3/sitepro_3.log" lines_diff = "200" />
    <output name="output" file="sitepro_3/sitepro_3_dump.txt" />
  </test>
  <test maxseconds="3600" name="Sitepro_4">
    <param name="mode_select" value="single" />
    <param name="wfile" value="wiggle.wig" />
    <param name="bfile" value="bedfile.bed" />
    <param name="span" value="100" />
    <param name="pfres" value="10" />
    <output name="output" file="sitepro_4/sitepro_4.pdf" />
    <output name="output" file="sitepro_4/sitepro_4.log" lines_diff = "200" />
    <output name="output" file="sitepro_4/sitepro_4_dump.txt" />
  </test>
  <test maxseconds="3600" name="Sitepro_5">
    <param name="mode_select" value="single" />
    <param name="wfile" value="wiggle.wig" />
    <param name="bfile" value="bedfile.bed" />
    <param name="span" value="5000" />
    <param name="pfres" value="500" />
    <output name="output" file="sitepro_5/sitepro_5.pdf" />
    <output name="output" file="sitepro_5/sitepro_5.log" lines_diff = "200" />
    <output name="output" file="sitepro_5/sitepro_5_dump.txt" />
  </test>
</tests>
  <help>
This tool draws the average score profile around given genomic
sites. It's a module in CEAS package which is written by Hyunjin Gene
Shin, published in Bioinformatics (pubmed id:19689956).

.. class:: infomark

**TIP #1:** If your query does not apper in the pulldown menu for BED Files, please convert your interval files to BED format.

.. class:: infomark

**TIP #2:** You can't use multiple BED files *AND* multiple Wiggle files as input. 

.. class:: infomark

**TIP #3:** The tool can be used to check the signals of your ChIP
sample around certain regions such as Transcription Start Sites, or
Transcription Factor Binding Sites.

.. class:: warningmark

**NEED IMPROVEMENT**

-----

**Parameters**

- **Sitepro behaviour mode** can only be '1 wiggle file against 1 BED
  file', or 'multiple wiggle files against 1 BED file', or '1 wiggle
  file against multiple BED files'.
- **Wiggle label** When 'multi wiggle' mode is selected, you need to assign the labels for every wiggle files which will be shown in the final figure.
- **BED label** When 'multi BED' mode is selected, you need to assign the labels for every BED files which will be shown in the final image.
- **Span** is the distance from the center of each BED region in both directions(+/-) (eg, [c - span, c + span], where c is the center of a region).
- **Profiling resolution** is the resolution to bin the scores in the final image.

-----

**script parameter list of Sitepro**

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -w WIG, --wig=WIG     input WIG file. WARNING: both fixedStep and
                        variableStep WIG formats are accepted. Multiple WIG
                        files can be given via -w (--wig) individually (eg -w
                        WIG1.wig, -w WIG2.wig). WARNING! multiple wig and bed
                        files are not allowed.
  -b BED, --bed=BED     BED file of regions of interest. (eg, binding sites or
                        motif locations) Multiple BED files can be given via
                        -b (--bed) individually (eg -b BED1.bed -b BED2.bed).
                        WARNING! multiple wig and bed files are not allowed.
  --span=SPAN           Span from the center of each BED region in both
                        directions(+/-) (eg, [c - span, c + span], where c is
                        the center of a region), default:1000 bp
  --pf-res=PF_RES       Profiling resolution, default: 50 bp
  --dir                 If set, the direction (+/-) is considered in
                        profiling. If no strand info given in the BED, this
                        option is ignored.
  --dump                If set, profiles are dumped as a TXT file
  --name=NAME           Name of this run. If not given, the body of the bed
                        file name will be used,
  -l LABEL, --label=LABEL
                        Labels of the wig files. If given, they are used as
                        the legends of the plot and in naming the TXT files of
                        profile dumps; otherwise, the WIG file names will be
                        used as the labels. Multiple labels can be given via
                        -l (--label) individually (eg, -l LABEL1 -l LABEL2).
                        WARNING! The number and order of the labels must be
                        the same as the WIG files.

-----

**Output**

- **PDF** format file.
- Dumped signals within given intervals in **plain text**.

  </help>

</tool>