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author modencode-dcc
date Fri, 18 Jan 2013 14:15:20 -0500
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<tool id="modencode_peakcalling_ranger" name="PeakRanger" version="1.16">
  <description>multi-purpose, ultrafast ChIP Seq peak caller</description>
  <command interpreter="python">ranger_wrapper.py $options_file $outputs_file</command>
  <requirements>
    <requirement type="package">peakranger</requirement>
  </requirements>
  <inputs>
    <param name="experiment_name" type="text" value="PeakRanger in Galaxy" size="50" label="Experiment Name"/>    

    <conditional name="major_command">
      <param name="major_command_selector" type="select" label="Select action to be performed">
        <option value="nr">Estimate data quality (nr)</option>
        <option value="lc">Calculate library complexity (lc)</option>
        <option value="wig">Generate coverage wiggle file (wig)</option>
        <option value="wigpe">Generate coverage wiggle file using block models (wigpe)</option>
        <option value="ranger">Peak calling for sharp peaks (ranger)</option>
        <option value="ccat">Peak calling for broad peaks (ccat)</option>
      </param>
      <when value="nr">
        <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
        <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />

        <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
      </when>
      <when value="lc">
        <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
      </when>
      <when value="wig">
        <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />

        <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>

        <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="output will be in .zip format (-s)"/>
        <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="output will be in .zip format (-x)"/>
        <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
      </when>
      <when value="wigpe">
        <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />

        <param name="extension" type="integer" value="0" label="Read extension length" help="default=0 (-l)"/>

        <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="(-s)"/>
        <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="(-x)"/>
        <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
      </when>
      <when value="ranger">
        <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
        <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />

	<conditional name="gene_annotate_file">
	  <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
	    <option value="dm3refGene.txt">dm3refGene.txt</option>
	    <option value="hg19refGene.txt">hg19refGene.txt</option>
	    <option value="mm9refGene.txt">mm9refGene.txt</option>
	    <option value="Upload">Select from history</option>
	    <option value="None">None</option>
	  </param>
	  <when value="upload">
            <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
	  </when>
	</conditional>
 	<param name="threads" type="integer" value="1" label="Number of threads" help="default=1 (-t)"/>
	<param name="plot_region" type="integer" value="6000" label="The length of the snapshot region in the HTML report" help="(--plot_region)"/>
        <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
	<param name="pvalue" type="float" value="0.0001" label="p-value cut-off" help="default=0.0001 (-p)"/>
	<param name="fdr" type="float" value="0.01" label="FDR cut-off" help="default=0.01 (-p)"/>
 	<param name="delta" type="integer" value="1" label="Sensitivity of the summit detector" help="default=1 (-r)"/>
        <param name="bandwith" type="integer" value="99" label="Smoothing bandwith" help="default=99 (-b)"/>

        <param name="pad" truevalue="--pad" falsevalue="" type="boolean" checked="False" label="Pad read coverage profile to avoid false positive summits" help="(--pad)"/>
      </when>
      <when value="ccat">
        <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
        <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />

	<conditional name="gene_annotate_file">
	  <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
	    <option value="dm3refGene.txt">dm3refGene.txt</option>
	    <option value="hg19refGene.txt">hg19refGene.txt</option>
	    <option value="mm9refGene.txt">mm9refGene.txt</option>
	    <option value="Upload">Select from history</option>
	    <option value="None">None</option>
	  </param>
	  <when value="upload">
            <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
	  </when>
	</conditional>
        <param name="plot_region" type="integer" value="6000" label="Read extension length" help="default=6000 (--plot_region)"/>
        <param name="extension" type="integer" value="100" label="Read extension length" help="default=100 (-l)"/>
        <param name="fdr" type="float" value="0.11" label="FDR cut-off" help="default=0.11 (-q)"/>
        <param name="winsize" type="integer" value="500" label="Sliding window size" help="default=500 (--win_size)"/>
        <param name="winstep" type="integer" value="50" label="Window moving step" help="default=50 (--win_step)"/>
        <param name="mincount" type="integer" value="4" label="Minimum window reads count" help="default=4 (--min_count)"/>
        <param name="minscore" type="integer" value="5" label="Minimum window reads fold change" help="default=5 (--min_score)"/>
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data name="output_ranger_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
        <filter>major_command['major_command_selector'] == 'nr' or major_command['major_command_selector'] == 'lc' or major_command['major_command_selector'] == 'ccat'</filter>
    </data>
    <data name="output_wigzip_file" format="wig, zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
        <filter>major_command['major_command_selector'] == 'wig' or major_command['major_command_selector'] == 'wigpe'</filter>
    </data>
    <data name="output_summit_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (summit)">
        <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
    </data>
    <data name="output_region_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (region)">
        <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
    </data>
    <data name="output_details_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (details)">
        <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
    </data>
    <data name="output_report_file" format="zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (html report)">
        <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
        <filter>major_command['gene_annotate_file']['gene_annotate_file_selector'] != 'None'</filter>
    </data>
  </outputs>

  <configfiles>
    <configfile name="outputs_file">&lt;%
import simplejson
%&gt;
##=======================================================================================
#set $__outputs = { 'command':str( $major_command.major_command_selector ) }
#if str( $major_command.major_command_selector ) == 'nr' or str( $major_command.major_command_selector ) == 'lc':
        #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
#end if
##=======================================================================================
#if str( $major_command.major_command_selector ) == 'wig' or str( $major_command.major_command_selector ) == 'wigpe':
        #set $__outputs['output_wigzip_file'] = str( $output_wigzip_file )
#end if
##=======================================================================================
#if str( $major_command.major_command_selector ) == 'ranger' or str( $major_command.major_command_selector ) == 'ccat':
        #set $__outputs['output_summit_file'] = str( $output_summit_file )
        #set $__outputs['output_region_file'] = str( $output_region_file )
        #set $__outputs['output_details_file'] = str( $output_details_file )
        #set $__outputs['output_report_file'] = str( $output_report_file )
        #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
#end if
##=======================================================================================
${ simplejson.dumps( __outputs ) }
    </configfile>
    <configfile name="options_file">&lt;%
import simplejson
%&gt;
#set $__options = { 'experiment_name':str($experiment_name), 'action':str( $major_command.major_command_selector ) }

##=============================================================================
#if str($major_command.major_command_selector) == 'nr':
	#set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
       	#set $__options['input_file'] = str( $major_command.input_control_file1 )

	#set $__options['extension'] = str( $major_command.extension )
#end if
##=============================================================================
##if str($major_command.major_command_selector) == 'lc':
        #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
##end if
##=============================================================================
#if str($major_command.major_command_selector) == 'wig' or str($major_command.major_command_selector) == 'wigpe':
        #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )

        #set $__options['extension'] = str( $major_command.extension )
        #set $__options['split'] = str( $major_command.split )
        #set $__options['strand'] = str( $major_command.strand)
        #set $__options['gzip'] = str( $major_command.gzip )
#end if
##=============================================================================
#if str($major_command.major_command_selector) == 'ranger':
        #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
       	#set $__options['input_file'] = str( $major_command.input_control_file1 )

        #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
	#if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
		#set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file ) 
	#end if

        #set $__options['plot_region'] = str( $major_command.plot_region )
        #set $__options['pvalue'] = str( $major_command.pvalue )
        #set $__options['fdr'] = str( $major_command.fdr )
        #set $__options['extension'] = str( $major_command.extension )
        #set $__options['delta'] = str( $major_command.delta )
	#set $__options['threads'] = str( $major_command.threads )
        #set $__options['bandwith'] = str( $major_command.bandwith )
        #set $__options['pad'] = str( $major_command.pad )
#end if
##=============================================================================
#if str($major_command.major_command_selector) == 'ccat':
        #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
      	#set $__options['input_file'] = str( $major_command.input_control_file1 )

        #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
	#if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
		#set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file ) 
	#end if

        #set $__options['plot_region'] = str( $major_command.plot_region )
        #set $__options['fdr'] = str( $major_command.fdr )
        #set $__options['extension'] = str( $major_command.extension )
        #set $__options['winsize'] = str( $major_command.winsize )
        #set $__options['winstep'] = str( $major_command.winstep )
        #set $__options['mincount'] = str( $major_command.mincount )
        #set $__options['minscore'] = str( $major_command.minscore )
#end if
##=============================================================================
${ simplejson.dumps( __options ) }
    </configfile>
  </configfiles>
  <tests>
	<!--none yet for macs2-->
  </tests>
  <help>
**What it does**

PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:

View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction

------

**Usage**

**nr:** noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment

**lc:** library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.

**wig:** coverage file generator. Generates variable step format wiggle file

**wigpe:** coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files

        wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.

**ranger:** ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.

**ccat:** ChIP-Seq peak caller. Tuned for the discovery of broad peaks

        Both ranger and ccat supports generating HTML-based annotation reports.

------

**Citation**

If you use PeakRanger in your research, please cite:
Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.

if you use the ccat tool, please also cite:
Xu, H., L. Handoko, et al. (2010).A signal-noise model for significance analysis of ChIP-seq with negative control.Bioinformatics 26(9): 1199-1204.


Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
  </help>
</tool>