# HG changeset patch
# User modencode-dcc
# Date 1358537828 18000
# Node ID e207763f91cbca834248baaa8eb3f62ee9d93d64
# Parent  390a709f0eca415553345d871f7873e657a10713
Deleted selected files

diff -r 390a709f0eca -r e207763f91cb ranger_wrapper.xml
--- a/ranger_wrapper.xml	Fri Jan 18 14:15:20 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,254 +0,0 @@
-<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>