# HG changeset patch
# User nikos
# Date 1409673604 14400
# Node ID eebdd6da935398810a14516a3fdf0c35b2efcc0b
# Parent 558f7f9baa78b3bb34796c4f687a65610b98554b
Deleted selected files
diff -r 558f7f9baa78 -r eebdd6da9353 bedClip.sh
--- a/bedClip.sh Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-bedClip $1 <(fetchChromSizes $2 2> /dev/null) $3
diff -r 558f7f9baa78 -r eebdd6da9353 bedClip.xml
--- a/bedClip.xml Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-
- Remove lines from bed file that refer to off-chromosome places.
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- ## Set genome assembly
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- #set $Genome = str( $genome_cond.genome )
- #if str( $genome_cond ) == 'OTHER':
- #set $Genome = str( $genome_cond.genome_other )
- #end if
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- bedClip.sh $input $Genome $output
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-**What it does**
-bedClip - Remove lines from bed file that refer to off-chromosome places.
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-**Usage**
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- bedClip input.bed chrom.sizes output.bed
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diff -r 558f7f9baa78 -r eebdd6da9353 bedExtendRanges.xml
--- a/bedExtendRanges.xml Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-
- Extend length of entries in bed 6+.
-
- ## Set genome assembly
-
- #set $Genome = str( $genome_cond.genome )
- #if str( $genome_cond ) == 'OTHER':
- #set $Genome = str( $genome_cond.genome_other )
- #end if
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- bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu $Genome $length $input 2> /dev/null > $output
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-**What it does**
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-bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,
-taking strand directionality into account.
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-**Usage**
-
- bedExtendRanges database length files(s)
-
-**Example**
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- * bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu hg18 250 stdin
-
- will transform:
- chr1 500 525 . 100 +
- chr1 1000 1025 . 100 -
- to:
- chr1 500 750 . 100 +
- chr1 775 1025 . 100 -
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diff -r 558f7f9baa78 -r eebdd6da9353 bigWigSummary.xml
--- a/bigWigSummary.xml Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-
- Extract summary information from a bigWig file.
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- bigWigSummary $input $chrom $start $end $dataPoints -type=$type> $output
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-**Usage**
- * bigWigSummary file.bigWig chrom start end dataPoints
- * Get summary data from bigWig for indicated region, broken into dataPoints equal parts. (Use dataPoints=1 for simple summary.)
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diff -r 558f7f9baa78 -r eebdd6da9353 bigwig2summary.xml
--- a/bigwig2summary.xml Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
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- Extract summary information from a bigWig file across multiple genomic regions specified by the user.
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- bigWigSummary
- bigwig2summary_stdout
- bedClip
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- /home/jens/bin/bigwig2summary_stdout -f $input_bw -b $input_bed -n $bins -o $assembly -t $type $header > $output
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-This tool extracts summary values (mean, min, max, std or coverage) from a **bigWig** file for a number of equal sized bins across genomic regions given in an a "BED-like" file.
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-The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigSummary_ and bedClip_.
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-.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary
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-.. _bedClip: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip
-
------
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-.. class:: infomark
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-The file contaning the genomic region must be TAB-delimited with at list 3 columns representing Chromosome, ChrStart and ChrEnd. If the file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed.
-
------
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-**Example 1**
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-Input BED file::
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- chr19 50178708 50180708
- chr6 90348174 90350174
- chr16 58495848 58497848
- chr5 180580242 180582242
- chr9 120177017 120179017
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-Extract summary (*#* of bins = 3)::
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- 0 0 0
- 0.144886 0 0
- 0.507327 1.14649 1.38456
- 0.221471 0.144886 0.309857
- 0.348944 0.426638 0.244495
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-**Example 2**
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-Input BED file (with strand information)::
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- chr19 50178708 50180708 NM_198318 0 + PRMT1
- chr6 90348174 90350174 NM_020466 0 - LYRM2
- chr16 58495848 58497848 NM_020465 0 + NDRG4
- chr5 180580242 180582242 NM_206880 0 + OR2V2
- chr9 120177017 120179017 NM_014010 0 - ASTN2
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-Extract summary (*#* of bins = 3)::
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- 0 0 0
- 0 0 0.144886
- 0.507327 1.14649 1.38456
- 0.221471 0.144886 0.309857
- 0.244495 0.426638 0.348944
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diff -r 558f7f9baa78 -r eebdd6da9353 make_ucsc_track.sh
--- a/make_ucsc_track.sh Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/bin/bash
-
-# This tool creates a UCSC track line given a bigWig or bedGraph input file, a track name and genome assembly.
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-## Define URL prefix
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-URL="http://data.bric.dk/galaxy/UCSC"
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-#parse input
-while getopts hi:t:n:o: myarg
-do case "$myarg" in
- h) echo "Usage: create UCSC track line -i -t -n -o "
- exit ;;
- i) input_file="$OPTARG" ;;
- t) file_type="$OPTARG" ;;
- n) track_name="$OPTARG" ;;
- o) org_assembly="$OPTARG" ;;
- [?]) echo "Usage: create UCSC track line -i -t -n -o "
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- exit 1 ;;
- esac
-done
-
-####################################################################
-# Check if a link to that file exists in the UCSC webfolder
-flag=0
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-for link in `ls -1 $UCSCPATH`
-do
- if [ `readlink -f $input_file` == `readlink -f $UCSCPATH/$link` ] ; then
- link_path=/$link # use already existing link
- flag=1
- fi
-done
-
-# If link to input file doesn't exist, create anonymous soft-link for input file in a folder accessible from the web.
-
-if [ $flag == 0 ]; then
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- link_path=`mktemp -u --tmpdir=/`
- ln -s $input_file $UCSCPATH$link_path
-fi
-
-####################################################################
-##Convert 4th character of file_type to uppercase (e.g. bigwig -> bigWig). UCSC browser doesn't recognize the file type otherwise.
-
-##Split file_type string to prefix (big) and suffix (wig, bed) and uppercase the first character of the latter.
-prefix=`echo ${file_type:0:3}`
-suffix=`echo ${file_type:3} | sed -e "s/\b\(.\)/\u\1/g"`
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-file_type=`echo ${prefix}${suffix}`
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-####################################################################
-#Contruct URL
-bigURL=`echo ${URL}${link_path}`
-
-####################################################################
-## Print track line
-echo "track name='$track_name' db=$org_assembly type=$file_type visibility=full alwaysZero=ON bigDataUrl=$bigURL"
diff -r 558f7f9baa78 -r eebdd6da9353 make_ucsc_track.xml
--- a/make_ucsc_track.xml Tue Jul 15 07:19:46 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-
- Create a track line to import a bigWig or bigBed file in the UCSC genome browser
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- make_ucsc_track.sh -i $input -t ${input.ext} -n '$name' -o $assembly > $output
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-This tool creates a UCSC track line for a bigWig or bigBed dataset in Galaxy. The text output can be pasted in the "Paste URLs or data" form in the `Add Custom Tracks`_ section of the UCSC Genome Browser.
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-.. _Add Custom Tracks: http://genome.ucsc.edu/cgi-bin/hgCustom
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