changeset 0:45f3fa82369f default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 18:08:31 -0400
parents
children
files Wig_to_bedGraph/README Wig_to_bedGraph/galaxy/Wig2bedGraph.xml Wig_to_bedGraph/script/wig2bedGraph_converter.pl Wig_to_bedGraph/t/hg17_chrY_pos.bed Wig_to_bedGraph/t/hg17_chrY_pos.wig
diffstat 5 files changed, 2166 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Wig_to_bedGraph/README	Tue Jun 07 18:08:31 2011 -0400
@@ -0,0 +1,41 @@
+INTRODUCTION
+
+A tool for converting data in wiggle fixedStep or variableStep format to four column bedGraph format 
+
+CONTENTS
+
+galaxy: Contains tool configuration file in *.xml format. 
+
+    Wig2bedGraph.xml
+
+t: Test data set. (move to your galaxy root folder/test-data/)
+    
+    You may need to move the test files into your test-data directory so galaxy can find them. 
+    If you want to run the functional tests eg as: 
+
+    sh run_functional_tests.sh -id fml_wig2bed 
+
+script: Perl based script.
+
+    wig2bedGraph_converter.pl: Read data in wiggle fixedStep and variableStep and convert to bedGraph format.
+    
+REQUIREMENTS
+
+    Perl
+
+COMMENTS/QUESTIONS 
+
+I can be reached at vipin.ts@tuebingen.mpg.de
+
+LICENSE
+
+Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or
+(at your option) any later version.
+
+COURTESY
+
+Galaxy Team.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Wig_to_bedGraph/galaxy/Wig2bedGraph.xml	Tue Jun 07 18:08:31 2011 -0400
@@ -0,0 +1,65 @@
+<tool id="fml_wig2bed" name="Wig_to_bedGraph" version="1.0.0">
+	<description>converter</description> 
+	<command interpreter="perl">wig2bedGraph_converter.pl $inf_wig > $bed_format 
+	</command> 
+	<inputs>
+  		<param format="wig" name="inf_wig" type="data" label="Convert this file" help="Data in fixedStep or variableStep wiggle format."/>
+        </inputs>
+  	<outputs>
+  		<data format="bed" name="bed_format" /> 
+  	</outputs>
+	    <tests>
+        	<test>
+                <param name="inf_wig" value="hg17_chrY_pos.wig" />
+                <output name="bed_format" file="hg17_chrY_pos.bed" />
+        	</test>
+        </tests>
+  	<help>
+
+**What it does**
+
+This tool converts data in wiggle fixedStep_ or variableStep_ format to four column bedGraph_ format.
+
+.. _fixedStep: http://genome.ucsc.edu/goldenPath/help/wiggle.html
+.. _variableStep: http://genome.ucsc.edu/goldenPath/help/wiggle.html
+.. _bedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
+
+--------
+
+**Example**
+
+- The following data in wiggle fixedStep format::
+
+	track type=wiggle_0 name="ARTS+ chrY" description="ARTS - TSS Finder - chrY - positive strand" visibility=full autoScale=on color=0,200,100 maxHeightPixels=300:150:50 graphType=bar yLineMark=0 yLineOnOff=on smoothingWindow=2
+	fixedStep chrom=chrY start=1151 step=50
+	-1.17966
+	-0.56397
+	-0.79706
+	-0.99435
+	-1.11338
+	-1.23153
+
+- Will be converted to bedGraph format::
+
+	chrY	1150	1151	-1.17966
+	chrY	1200	1201	-0.56397
+	chrY	1250	1251	-0.79706
+	chrY	1300	1301	-0.99435
+	chrY	1350	1351	-1.11338
+	chrY	1400	1401	-1.23153
+
+--------
+
+**About formats**
+
+**Wiggle (variableStep)** The data is introduced by a line beginning with the keyword "variableStep", and the arguments "chrom" and "span", which indicate the chromosome on which the features are located, and the width of each feature, in base pairs. This is followed by a series of two-element lines indicating the start position of each feature, and its quantitative value. Values can be any sort of numeric data, including integers, negative numbers and floating point.
+
+**Wiggle (fixedStep)** The data is introduced by a line beginning with the keyword "fixedStep", and the arguments "chrom", "span", "start" and "step". The first two arguments are the same as wiggle variableStep, while "start" and "step" indicate the starting position of the first feature, and the spacing between each feature. This is followed by a numeric value for each step.
+
+**bedGraph** There are four required fields: ref_sequence,start,end and score. Note that here the coordinates are "zero-indexed", half open, which means the start coordinate is zero-indexed and the end coordinate is 1-indexed.
+
+--------
+
+This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010-2011 Max Planck Society
+	</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Wig_to_bedGraph/script/wig2bedGraph_converter.pl	Tue Jun 07 18:08:31 2011 -0400
@@ -0,0 +1,62 @@
+#!/usr/bin/env perl
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# Written (W) 2010 Vipin T. Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society
+# Copyright (C) 2010 Max Planck Society
+#
+# Description: - read fixedStep and variableStep wiggle input data,
+#		output four column bedGraph format data
+
+use warnings;
+use strict;
+
+my ($position, $chr, $step, $span) = (0, "", 1, 1);
+
+my $usage = q(
+fixedStep2BED.pl  - Program to convert a valid fixedStep or variableStep wiggle input data to BED format.
+USAGE: wig2bedGraph_converter <fixedStep/variableStep Wiggle format> > <output file name>
+
+);
+if (scalar(@ARGV) != 1) {
+    print $usage;
+    exit
+}
+
+my $inFile = $ARGV[0];
+open WIG, "<$inFile" || die "Can't open the Wiggle file \n";
+while (my $dataValue = <WIG>)
+{
+    chomp $dataValue;
+    next if ( $dataValue =~ m/^track /);
+    if ( $dataValue =~ m/^fixedStep/ || $dataValue =~ m/^variableStep/ ) {
+        ($position, $chr, $step, $span) = (0, "", 1, 1);
+        my @a = split('\s', $dataValue);
+        for (my $i = 1; $i < scalar(@a); ++$i) {
+            my ($ident, $value) = split('=',$a[$i]);
+            if ($ident =~ m/chrom/) { $chr = $value; }
+            elsif ($ident =~ m/start/) { $position = $value-1; }
+            elsif ($ident =~ m/step/) { $step = $value; }
+            elsif ($ident =~ m/span/) { $span = $value; }
+            else {
+                print STDERR "ERROR: unrecognized fixedStep/variableStep line: $dataValue\n";
+                exit 255;
+            }
+        }
+    } 
+    else {
+        my @b = split('\s', $dataValue);
+        if (scalar(@b)>1) {
+            $position = $b[0];
+            $dataValue = $b[1];
+        }
+        my $loc_pos = $position+$span;
+        print "$chr\t$position\t$loc_pos\t$dataValue\n";
+        $position = $position + $step;
+    }
+}
+close WIG;
+exit;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Wig_to_bedGraph/t/hg17_chrY_pos.bed	Tue Jun 07 18:08:31 2011 -0400
@@ -0,0 +1,998 @@
+chrY	0	1	-1000.00000
+chrY	50	51	-1000.00000
+chrY	100	101	-1000.00000
+chrY	150	151	-1000.00000
+chrY	200	201	-1000.00000
+chrY	250	251	-1000.00000
+chrY	300	301	-1000.00000
+chrY	350	351	-1000.00000
+chrY	400	401	-1000.00000
+chrY	450	451	-1000.00000
+chrY	500	501	-1000.00000
+chrY	550	551	-1000.00000
+chrY	600	601	-1000.00000
+chrY	650	651	-1000.00000
+chrY	700	701	-1000.00000
+chrY	750	751	-1000.00000
+chrY	800	801	-1000.00000
+chrY	850	851	-1000.00000
+chrY	900	901	-1000.00000
+chrY	950	951	-1000.00000
+chrY	1000	1001	-1000.00000
+chrY	1050	1051	-1000.00000
+chrY	1100	1101	-1000.00000
+chrY	1150	1151	-1.17966
+chrY	1200	1201	-0.56397
+chrY	1250	1251	-0.79706
+chrY	1300	1301	-0.99435
+chrY	1350	1351	-1.11338
+chrY	1400	1401	-1.23153
+chrY	1450	1451	-1.23723
+chrY	1500	1501	-0.85183
+chrY	1550	1551	-0.91563
+chrY	1600	1601	-0.70372
+chrY	1650	1651	-1.12867
+chrY	1700	1701	-1.07815
+chrY	1750	1751	-0.98988
+chrY	1800	1801	-0.69262
+chrY	1850	1851	-0.35994
+chrY	1900	1901	-0.20062
+chrY	1950	1951	-0.21524
+chrY	2000	2001	-0.24273
+chrY	2050	2051	-0.32931
+chrY	2100	2101	-0.62261
+chrY	2150	2151	-0.72635
+chrY	2200	2201	-0.08683
+chrY	2250	2251	0.35553
+chrY	2300	2301	-0.49693
+chrY	2350	2351	-0.06360
+chrY	2400	2401	-0.47514
+chrY	2450	2451	-0.20126
+chrY	2500	2501	-0.18858
+chrY	2550	2551	-0.44872
+chrY	2600	2601	-0.12142
+chrY	2650	2651	-0.11963
+chrY	2700	2701	-0.52232
+chrY	2750	2751	-0.41265
+chrY	2800	2801	-0.48277
+chrY	2850	2851	-0.23210
+chrY	2900	2901	-0.14889
+chrY	2950	2951	-0.26716
+chrY	3000	3001	0.50460
+chrY	3050	3051	0.37151
+chrY	3100	3101	-0.42917
+chrY	3150	3151	-0.47050
+chrY	3200	3201	-0.48072
+chrY	3250	3251	-0.62466
+chrY	3300	3301	-0.24647
+chrY	3350	3351	-0.30284
+chrY	3400	3401	-0.26817
+chrY	3450	3451	-0.08717
+chrY	3500	3501	0.18104
+chrY	3550	3551	0.19199
+chrY	3600	3601	0.15381
+chrY	3650	3651	-0.04370
+chrY	3700	3701	0.02108
+chrY	3750	3751	0.28373
+chrY	3800	3801	-0.24397
+chrY	3850	3851	-0.21994
+chrY	3900	3901	-0.37915
+chrY	3950	3951	-0.09437
+chrY	4000	4001	-0.00153
+chrY	4050	4051	0.03517
+chrY	4100	4101	0.10660
+chrY	4150	4151	0.17470
+chrY	4200	4201	-0.04983
+chrY	4250	4251	0.02838
+chrY	4300	4301	0.25037
+chrY	4350	4351	-0.21384
+chrY	4400	4401	0.07358
+chrY	4450	4451	0.01191
+chrY	4500	4501	0.08469
+chrY	4550	4551	0.17259
+chrY	4600	4601	-0.10388
+chrY	4650	4651	-0.42776
+chrY	4700	4701	-0.11207
+chrY	4750	4751	-0.20124
+chrY	4800	4801	-0.49159
+chrY	4850	4851	-0.95681
+chrY	4900	4901	-1.04134
+chrY	4950	4951	-1.27021
+chrY	5000	5001	-1.42443
+chrY	5050	5051	-1.51322
+chrY	5100	5101	-1.64583
+chrY	5150	5151	-1.05135
+chrY	5200	5201	-1.04954
+chrY	5250	5251	-1.13581
+chrY	5300	5301	-1.18998
+chrY	5350	5351	-1.09437
+chrY	5400	5401	-0.96355
+chrY	5450	5451	-1.10489
+chrY	5500	5501	-0.87685
+chrY	5550	5551	-1.35273
+chrY	5600	5601	-0.62571
+chrY	5650	5651	-1.04302
+chrY	5700	5701	-1.02615
+chrY	5750	5751	-0.35145
+chrY	5800	5801	-0.94946
+chrY	5850	5851	-0.34520
+chrY	5900	5901	-0.42208
+chrY	5950	5951	-0.67363
+chrY	6000	6001	0.07613
+chrY	6050	6051	0.25426
+chrY	6100	6101	0.28458
+chrY	6150	6151	0.12299
+chrY	6200	6201	-0.46344
+chrY	6250	6251	-0.37632
+chrY	6300	6301	-0.69721
+chrY	6350	6351	-0.63100
+chrY	6400	6401	-0.81136
+chrY	6450	6451	-0.70704
+chrY	6500	6501	-0.48391
+chrY	6550	6551	-0.37131
+chrY	6600	6601	-0.45360
+chrY	6650	6651	-0.34665
+chrY	6700	6701	0.32367
+chrY	6750	6751	-0.28257
+chrY	6800	6801	-0.12696
+chrY	6850	6851	-0.18846
+chrY	6900	6901	-0.21782
+chrY	6950	6951	-0.45364
+chrY	7000	7001	-0.15734
+chrY	7050	7051	-0.22713
+chrY	7100	7101	-0.27517
+chrY	7150	7151	-0.06162
+chrY	7200	7201	-0.31208
+chrY	7250	7251	-0.33731
+chrY	7300	7301	-0.23307
+chrY	7350	7351	-0.02035
+chrY	7400	7401	-0.19164
+chrY	7450	7451	-0.12095
+chrY	7500	7501	-0.28241
+chrY	7550	7551	-0.35123
+chrY	7600	7601	-0.17881
+chrY	7650	7651	-0.51819
+chrY	7700	7701	-0.59634
+chrY	7750	7751	-0.83821
+chrY	7800	7801	-0.66985
+chrY	7850	7851	-0.90570
+chrY	7900	7901	-0.90672
+chrY	7950	7951	-0.96593
+chrY	8000	8001	-0.75810
+chrY	8050	8051	-0.93543
+chrY	8100	8101	-0.89678
+chrY	8150	8151	-0.93989
+chrY	8200	8201	-0.95575
+chrY	8250	8251	-0.78583
+chrY	8300	8301	-0.79166
+chrY	8350	8351	-0.81385
+chrY	8400	8401	-0.65868
+chrY	8450	8451	-0.56644
+chrY	8500	8501	-0.37303
+chrY	8550	8551	-0.62309
+chrY	8600	8601	-0.57250
+chrY	8650	8651	-0.32212
+chrY	8700	8701	-0.21982
+chrY	8750	8751	-0.10352
+chrY	8800	8801	-0.49088
+chrY	8850	8851	-0.50410
+chrY	8900	8901	-0.59987
+chrY	8950	8951	-0.44954
+chrY	9000	9001	-0.20355
+chrY	9050	9051	-0.22377
+chrY	9100	9101	0.15516
+chrY	9150	9151	0.68232
+chrY	9200	9201	0.52046
+chrY	9250	9251	0.64105
+chrY	9300	9301	0.76313
+chrY	9350	9351	0.28916
+chrY	9400	9401	0.69376
+chrY	9450	9451	0.55557
+chrY	9500	9501	0.95737
+chrY	9550	9551	1.10034
+chrY	9600	9601	0.86026
+chrY	9650	9651	0.84377
+chrY	9700	9701	1.02491
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+chrY	9800	9801	1.10348
+chrY	9850	9851	1.25710
+chrY	9900	9901	1.08850
+chrY	9950	9951	0.52293
+chrY	10000	10001	0.67975
+chrY	10050	10051	0.35971
+chrY	10100	10101	0.55417
+chrY	10150	10151	-0.06260
+chrY	10200	10201	0.43237
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+chrY	11050	11051	-0.64841
+chrY	11100	11101	-1.29395
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+chrY	11200	11201	-0.88730
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+chrY	14200	14201	-0.74612
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+chrY	14900	14901	-1.37204
+chrY	14950	14951	-1.08069
+chrY	15000	15001	-0.87128
+chrY	15050	15051	-1.16748
+chrY	15100	15101	-1.19945
+chrY	15150	15151	-1.01292
+chrY	15200	15201	-1.43688
+chrY	15250	15251	-1.63166
+chrY	15300	15301	-1.55459
+chrY	15350	15351	-1.18872
+chrY	15400	15401	-1.12435
+chrY	15450	15451	-1.24636
+chrY	15500	15501	-1.14115
+chrY	15550	15551	-1.08633
+chrY	15600	15601	-0.77297
+chrY	15650	15651	-1.10362
+chrY	15700	15701	-0.90504
+chrY	15750	15751	-0.75526
+chrY	15800	15801	-0.81503
+chrY	15850	15851	-0.84651
+chrY	15900	15901	-0.58490
+chrY	15950	15951	-0.99376
+chrY	16000	16001	-1.09509
+chrY	16050	16051	-0.75380
+chrY	16100	16101	-0.81083
+chrY	16150	16151	-0.76614
+chrY	16200	16201	-0.80640
+chrY	16250	16251	-1.07450
+chrY	16300	16301	-1.18545
+chrY	16350	16351	-1.12080
+chrY	16400	16401	-1.41013
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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