Mercurial > repos > idot > fastx_toolkit2
view fastx_uncollapser.xml @ 1:e7c65e398bdd draft default tip
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author | idot |
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date | Wed, 10 Jul 2013 06:16:21 -0400 |
parents | 78a7d28f2a15 |
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<tool id="cshl_fastx_uncollapser" name="Uncollapse" version="1.0.0"> <description>sequences</description> <command> cat '$input' | fastx_uncollapser -v -o '$output' </command> <inputs> <param format="fasta" name="input" type="data" label="Collapsed FASTA file" /> </inputs> <tests> <test> <param name="input" value="fasta_uncollapser1.fasta" /> <output name="output" file="fasta_uncollapser1.out" /> </test> </tests> <outputs> <data format="fasta" name="output" metadata_source="input" /> </outputs> <help> **What it does** This tool uncollapses a previously-collapsed FASTA file. It reads each collapsed sequence and generates multiple sequences based on the collapsed read count. -------- **Example** Example Input - a collapsed FASTA file (Sequence "ATAT" has four collapsed reads):: >1-1 TGCG >2-4 ATAT Example Output - uncollapsed FASTA file (Sequence "ATAT" now appears as 4 separate sequences):: >1 TGCG >2 ATAT >3 ATAT >4 ATAT >5 ATAT .. class:: infomark The original sequence id (with the read counts) are discarded, with the sequence given a numerical name. ----- This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool> <!-- FASTX-Uncollapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->