Mercurial > repos > saket-choudhary > merge_columns_with_delimiter
view merge_columns_with_delimiter/merge_columns_with_delimiter.xml @ 0:eaf7c9b0a1a4 draft default tip
Uploaded
author | saket-choudhary |
---|---|
date | Tue, 07 Oct 2014 19:38:23 -0400 |
parents | |
children |
line wrap: on
line source
<tool id="merge_cols_with_delimiter1" name="Merge Columns with Delimiters" version="1.0.1"> <description>together</description> <command interpreter="python"> merge_columns_with_delimiter.py $input1 $out_file1 $delimiter $col1 $col2 #for $col in $columns ${col.datacol} #end for </command> <inputs> <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> <param name="delimiter" type="select" label="Delimiter"> <option value="s">Whitespaces</option> <option value="T">Tabs</option> <option value="Ep">EmptyString</option> <option value="Dt">Dots</option> <option value="C">Commas</option> <option value="D">Dashes</option> <option value="Sl">Left Slashes</option> <option value="Sr">Right Slashes</option> <option value="U">Underscores</option> <option value="P">Pipes</option> <option value="Co">Colons</option> <option value="Sc">Semicolons</option> </param> <param name="col1" label="Merge column" type="data_column" data_ref="input1" /> <param name="col2" label="with column" type="data_column" data_ref="input1" help="Need to add more columns? Use controls below."/> <repeat name="columns" title="Columns"> <param name="datacol" label="Add column" type="data_column" data_ref="input1" /> </repeat> </inputs> <outputs> <data format="tabular" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="merge_columns_with_delimiter_input.tsv"/> <param name="delimiter" value="D" /> <param name="col1" value="5" /> <param name="col2" value="1" /> <param name="datacol" value="3" /> <output name="out_file1" file="merge_columns_with_delimiter_output.tsv"/> </test> </tests> <help> .. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* ----- **What it does** This tool merges columns together separating them with the specified delimiter. Any number of valid columns can be merged in any order. Tool and code inspired from 'merge_columns' tool distributed with Galaxy. ----- **Example** Input dataset (five columns: c1, c2, c3, c4, and c5):: 1 10 1000 gene1 chr 2 100 1500 gene2 chr merging columns "**c5,c1**" with "-"(dash) will return:: 1 10 1000 gene1 chr chr-1 2 100 1500 gene2 chr chr-2 .. class:: warningmark Note that all original columns are preserved and the result of merge is added as the rightmost column. </help> </tool>