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80 lines
2.8 KiB
XML
80 lines
2.8 KiB
XML
<tool id="cshl_fasta_formatter" name="FASTA Width">
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<description>formatter</description>
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<!--
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Note:
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fasta_formatter also has a tabular output mode (-t),
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but Galaxy already contains such a tool, so no need
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to offer the user a duplicated tool.
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So this XML tool only changes the width (line-wrapping) of a
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FASTA file.
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-->
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<command>zcat -f '$input' | fasta_formatter -w $width -o $output</command>
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<inputs>
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<param format="fasta" name="input" type="data" label="Library to re-format" />
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<param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
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</inputs>
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<tests>
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<test>
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<!-- Re-format a FASTA file into a single line -->
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<param name="input" value="fasta_formatter1.fasta" />
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<param name="width" value="0" />
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<output name="output" file="fasta_formatter1.out" />
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</test>
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<test>
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<!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
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<param name="input" value="fasta_formatter1.fasta" />
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<param name="width" value="60" />
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<output name="output" file="fasta_formatter2.out" />
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</test>
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</tests>
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<outputs>
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<data format="input" name="output" metadata_source="input" />
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</outputs>
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<help>
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**What it does**
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This tool re-formats a FASTA file, changing the width of the nucleotides lines.
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**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
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--------
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**Example**
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Input FASTA file (each nucleotides line is 50 characters long)::
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>Scaffold3648
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AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
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CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
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TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
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ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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>Scaffold9299
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CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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aactggtctttacctTTAAGTTG
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Output FASTA file (with width=80)::
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>Scaffold3648
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AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
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ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
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ATTTTAATGAACATGTAGTAAAAACT
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>Scaffold9299
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CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
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GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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Output FASTA file (with width=0 => single line)::
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>Scaffold3648
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AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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>Scaffold9299
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CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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</help>
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</tool>
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