# HG changeset patch
# User nikos
# Date 1406894820 14400
# Node ID 52e9cfd72b2109cf48ca720aeedb37b7ca932505
# Parent  41e2861b6ab79ff039aa62e9511d7c547f8e98c3
Deleted selected files

diff -r 41e2861b6ab7 -r 52e9cfd72b21 bigwig_to_wig/bigwig_to_wig.sh
--- a/bigwig_to_wig/bigwig_to_wig.sh	Fri Aug 01 08:06:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#!/bin/bash
-#$Id: bigwig2wig 23 2014-01-28 12:09:22Z jens $
-
-#SCRIPT CONVERTS BIGWIG FILE TO FIXED-STEP WIGGLE FORMAT FILE
-#RESOLUTION IS CONTROLLED THROUGH THE BIN SIZE
-
-#default bin_size
-bin_size=500
-mylab="wiggle file"
-
-#parse input
-while getopts hf:b:l: myarg
-do	case "$myarg" in
-	h)	echo "Usage: bigwig_correlation -f <bigwig_file> -b <bin_size>"
-	        echo "Ex: bigwig_correlation -f <MYFILE.bw> -b 600"
-		exit ;;
-	f)	bigwig_file="$OPTARG" ;; #required
-	l)	mylab="$OPTARG" ;; #optional 
-	b)	bin_size="$OPTARG" ;; #optional
-	[?])	echo "Usage: bigwig_correlation -f <MYFILE.bw> -b <bin_size>"
-		exit 1 ;;
-	esac
-done
-
-###################################################
-###VALIDATE INPUT
-###################################################
-
-#make tmp-filename to hold chromosome info
-org_assembly_file=`mktemp -u`
-bigWigInfo -chroms $bigwig_file | perl -ne "/^\tchr/ && print" | perl -pe "s/ +/\t/g" | cut -f2,4 > $org_assembly_file
-
-#check bin_size & define step_size
-bin_size_mod=`expr $bin_size % 2`  #determine modulus
-if [ $bin_size_mod -ne 0 ]; then
-  echo "Chosen bin_size must be an even positive number, added +1 to bin_size"
-  bin_size=$(($bin_size + 1))
-fi
-
-if [ $bin_size -lt 100 ]; then
-  echo "ERROR: Chosen bin_size must be a positive number >=100"
-  exit 1
-fi
-#set stetp size equal to bin size i.e. non-overlapping intervals
-step_size=$bin_size
-
-###################################################
-###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILES
-###################################################
-
-
-#make track definition line
-echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\"" 
-
-#for each chromsome
-cat $org_assembly_file | while read line; do
- 
-  cur_chr=`echo $line | cut --delimiter=" " -f1`
-  cur_length=`echo $line | cut --delimiter=" " -f2`
-  
-  n_bins=`echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc`
- 
-  start=1
-  stop=`echo "$n_bins * $bin_size" | bc`
-
-  #write header line for each chromosome
-  echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size"
-  
-  #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins)
-  nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/" 
-  #gives warning if no data in/for current chromosome
-  
-done
-
-#rm tmp
-rm $org_assembly_file
-
diff -r 41e2861b6ab7 -r 52e9cfd72b21 bigwig_to_wig/bigwig_to_wig.xml
--- a/bigwig_to_wig/bigwig_to_wig.xml	Fri Aug 01 08:06:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.0">
-    <description>converter</description>
-    <command>bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command>
-  <requirements>
-      <requirement type="package">bigWigSummary</requirement>
-      <requirement type="package">bigWigInfo</requirement>
-  </requirements>
-  <inputs>
-      <param format="bigwig" name="input" type="data" label="BigWig file to convert" />
-      <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." />
-      <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" />
-  </inputs>
-  <outputs>
-      <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" />
-  </outputs>
-  <tests>
-      <test>
-	  <param name="input" value="1.bigwig" />
-	  <param name="bin_size" value="500" />
-	  <output name="output" file="1.wig" />	  
-      <test>
-  </tests>
-  <help>
-
-This tool converts a **BigWig** file to fixed step **Wiggle** format. 
-Resolution is controlled through the bin size (the higher the size, the lower the resolution).
-
-The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_.
-
-.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo
-.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary
-
-</help>
-</tool>
diff -r 41e2861b6ab7 -r 52e9cfd72b21 bigwig_to_wig/test-data/1.bigwig
Binary file bigwig_to_wig/test-data/1.bigwig has changed
diff -r 41e2861b6ab7 -r 52e9cfd72b21 bigwig_to_wig/tool_dependencies.xml
--- a/bigwig_to_wig/tool_dependencies.xml	Fri Aug 01 08:06:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bigWigSummary">
-        <install version="1.0">
-	    <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_binary"><url_template>http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary</url_template></action>
-	            <action type="move_directory_files">
-            		<source_directory>.</source_directory>
-            		<destination_directory>$INSTALL_DIR</destination_directory>
-        	    </action>
-		</actions>
-
-
-		<action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-        </readme>
-    </package>
-    <package name="bigWigInfo">
-        <install version="1.0">
-            <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_binary"><url_template>http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template></action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-
-
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>