Mercurial > repos > devteam > add_value
changeset 0:787fa5c2c738 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 11:15:22 -0500 |
| parents | |
| children | 4c6ec423baae |
| files | fixedValueColumn.pl fixedValueColumn.xml test-data/1.bed test-data/eq-addvalue.dat |
| diffstat | 4 files changed, 225 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fixedValueColumn.pl Mon Nov 09 11:15:22 2015 -0500 @@ -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;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fixedValueColumn.xml Mon Nov 09 11:15:22 2015 -0500 @@ -0,0 +1,61 @@ +<tool id="addValue" name="Add column" version="1.0.0"> + <description>to an existing dataset</description> + <command interpreter="perl">fixedValueColumn.pl "${input}" "${out_file1}" "${exp}" "${iterate}"</command> + <inputs> + <param name="exp" 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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