[2] | 1 | <tool id="cshl_fasta_formatter" name="FASTA Width"> |
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| 2 | <description>formatter</description> |
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| 3 | <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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| 4 | <!-- |
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| 5 | Note: |
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| 6 | fasta_formatter also has a tabular output mode (-t), |
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| 7 | but Galaxy already contains such a tool, so no need |
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| 8 | to offer the user a duplicated tool. |
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| 9 | |
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| 10 | So this XML tool only changes the width (line-wrapping) of a |
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| 11 | FASTA file. |
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| 12 | --> |
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| 13 | <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command> |
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| 14 | <inputs> |
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| 15 | <param format="fasta" name="input" type="data" label="Library to re-format" /> |
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| 16 | |
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| 17 | <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> |
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| 18 | </inputs> |
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| 19 | |
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| 20 | <tests> |
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| 21 | <test> |
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| 22 | <!-- Re-format a FASTA file into a single line --> |
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| 23 | <param name="input" value="fasta_formatter1.fasta" /> |
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| 24 | <param name="width" value="0" /> |
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| 25 | <output name="output" file="fasta_formatter1.out" /> |
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| 26 | </test> |
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| 27 | <test> |
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| 28 | <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> |
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| 29 | <param name="input" value="fasta_formatter1.fasta" /> |
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| 30 | <param name="width" value="60" /> |
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| 31 | <output name="output" file="fasta_formatter2.out" /> |
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| 32 | </test> |
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| 33 | </tests> |
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| 34 | |
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| 35 | <outputs> |
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| 36 | <data format="input" name="output" metadata_source="input" /> |
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| 37 | </outputs> |
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| 38 | |
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| 39 | <help> |
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| 40 | **What it does** |
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| 41 | |
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| 42 | This tool re-formats a FASTA file, changing the width of the nucleotides lines. |
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| 43 | |
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| 44 | **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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| 45 | |
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| 46 | -------- |
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| 47 | |
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| 48 | **Example** |
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| 49 | |
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| 50 | Input FASTA file (each nucleotides line is 50 characters long):: |
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| 51 | |
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| 52 | >Scaffold3648 |
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| 53 | AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC |
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| 54 | CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG |
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| 55 | TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA |
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| 56 | ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT |
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| 57 | >Scaffold9299 |
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| 58 | CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG |
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| 59 | TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG |
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| 60 | aactggtctttacctTTAAGTTG |
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| 61 | |
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| 62 | |
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| 63 | Output FASTA file (with width=80):: |
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| 64 | |
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| 65 | >Scaffold3648 |
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| 66 | AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT |
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| 67 | ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA |
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| 68 | ATTTTAATGAACATGTAGTAAAAACT |
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| 69 | >Scaffold9299 |
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| 70 | CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC |
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| 71 | GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG |
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| 72 | |
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| 73 | Output FASTA file (with width=0 => single line):: |
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| 74 | |
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| 75 | >Scaffold3648 |
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| 76 | AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT |
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| 77 | >Scaffold9299 |
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| 78 | CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG |
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| 79 | </help> |
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| 80 | </tool> |
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