Mercurial > repos > devteam > fasta_filter_by_length
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit 66d6c3cbb835114dc80e61216756e90da156f6d6"
author | devteam |
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date | Tue, 17 Dec 2019 13:13:32 -0500 |
parents | 2fd6033d0e9c |
children | 8cacfcf96a52 |
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<tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1"> <description></description> <command> python $__tool_directory__/fasta_filter_by_length.py '$input' $min_length $max_length '$output' </command> <inputs> <param name="input" type="data" format="fasta" label="Fasta file"/> <param name="min_length" type="integer" value="0" label="Minimal length" /> <param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> </inputs> <outputs> <data name="output" format="fasta"/> </outputs> <tests> <test> <param name="input" value="454.fasta" /> <param name="min_length" value="10" /> <param name="max_length" value="0" /> <output name="output" file="fasta_tool_filter_length_1.out" /> </test> <test> <param name="input" value="4.fasta" /> <param name="min_length" value="0" /> <param name="max_length" value="60" /> <output name="output" file="fasta_tool_filter_length_2.out" /> </test> </tests> <help> .. class:: infomark **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'. ----- **What it does** Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. ----- **Example** Suppose you have the following FASTA formatted sequences:: >seq1 TCATTTAATGAC >seq2 ATGGC >seq3 TCACATGATGCCG >seq4 ATGGAAGC Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp:: >seq1 TCATTTAATGAC >seq3 TCACATGATGCCG </help> </tool>