| Next changeset 1:4676e145a44e (2013-04-01) |
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Commit message:
Uploaded add_value tarball. |
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added:
fixedValueColumn.pl fixedValueColumn.xml test-data/1.bed test-data/eq-addvalue.dat |
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| diff -r 000000000000 -r 181dd378275c fixedValueColumn.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fixedValueColumn.pl Tue Dec 04 10:37:05 2012 -0500 |
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| @@ -0,0 +1,34 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# fixedValueColumn.pl $input $out_file1 "expression" "iterate [yes|no]" + +my ($input, $out_file1, $expression, $iterate) = @ARGV; +my $i = 0; +my $numeric = 0; + +die "Check arguments\n" unless @ARGV == 4; + +open (DATA, "<$input") or die "Cannot open $input:$!\n"; +open (OUT, ">$out_file1") or die "Cannot create $out_file1:$!\n"; + +if ($expression =~ m/^\d+$/) { + $numeric = 1; + $i = $expression; +} + +while (<DATA>) { + chop; + if ($iterate eq "no") { + print OUT "$_\t$expression\n"; + } else { + print OUT "$_\t$i\n" if $numeric == 1; + print OUT "$_\t$expression-$i\n" if $numeric == 0; + ++$i; + } +} + +close DATA; +close OUT; |
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| diff -r 000000000000 -r 181dd378275c fixedValueColumn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fixedValueColumn.xml Tue Dec 04 10:37:05 2012 -0500 |
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| @@ -0,0 +1,61 @@ +<tool id="addValue" name="Add column"> + <description>to an existing dataset</description> + <command interpreter="perl">fixedValueColumn.pl $input $out_file1 "$exp" $iterate</command> + <inputs> + <param name="exp" size="20" type="text" value="1" label="Add this value"/> + <param format="tabular" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" /> + <param name="iterate" type="select" label="Iterate?"> + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="exp" value="1"/> + <param name="input" value="1.bed"/> + <param name="iterate" value="no"/> + <output name="out_file1" file="eq-addvalue.dat"/> + </test> + </tests> + <help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +----- + +**What it does** + +You can enter any value and it will be added as a new column to your dataset + +----- + +**Example** + +If you original data looks like this:: + + chr1 10 100 geneA + chr2 200 300 geneB + chr2 400 500 geneC + +Typing **+** in the text box will generate:: + + chr1 10 100 geneA + + chr2 200 300 geneB + + chr2 400 500 geneC + + + +You can also add line numbers by selecting **Iterate: YES**. In this case if you enter **1** in the text box you will get:: + + chr1 10 100 geneA 1 + chr2 200 300 geneB 2 + chr2 400 500 geneC 3 + + + +</help> +</tool> |
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| diff -r 000000000000 -r 181dd378275c test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Dec 04 10:37:05 2012 -0500 |
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| @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - |
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| diff -r 000000000000 -r 181dd378275c test-data/eq-addvalue.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eq-addvalue.dat Tue Dec 04 10:37:05 2012 -0500 |
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| @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 1 +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 1 +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 1 +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 1 +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1 +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 1 +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 1 +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 1 +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 1 +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 1 +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + 1 +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - 1 +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - 1 +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + 1 +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - 1 +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + 1 +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + 1 +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - 1 +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + 1 +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - 1 +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - 1 +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + 1 +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - 1 +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + 1 +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + 1 +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - 1 +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + 1 +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - 1 +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + 1 +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - 1 +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + 1 +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - 1 +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - 1 +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + 1 +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - 1 +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + 1 +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + 1 +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - 1 +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + 1 +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - 1 +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + 1 +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - 1 +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + 1 +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - 1 +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + 1 +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - 1 +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + 1 +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - 1 +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - 1 +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + 1 +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - 1 +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + 1 +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + 1 +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - 1 +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + 1 +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - 1 +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - 1 +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + 1 +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - 1 +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + 1 +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - 1 +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + 1 +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - 1 +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + 1 +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - 1 |