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annotate fasta_formatter.xml @ 2:9457a20156db draft
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author | devteam |
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date | Mon, 12 Oct 2015 10:15:31 -0400 |
parents | 1dbb5181c327 |
children | 859422bcb689 |
rev | line source |
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0 | 1 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> |
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2 <description>formatter</description> |
0 | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
5 </requirements> | |
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6 <!-- |
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7 Note: |
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8 fasta_formatter also has a tabular output mode (-t), |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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9 but Galaxy already contains such a tool, so no need |
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10 to offer the user a duplicated tool. |
0 | 11 |
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12 So this XML tool only changes the width (line-wrapping) of a |
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13 FASTA file. |
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14 --> |
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15 <command> |
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16 <![CDATA[ |
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17 zcat -f < '$input' | fasta_formatter -w $width -o '$output' |
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18 ]]> |
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19 </command> |
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20 <inputs> |
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21 <param format="fasta" name="input" type="data" label="Library to re-format" /> |
0 | 22 |
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23 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> |
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24 </inputs> |
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25 <outputs> |
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26 <data format="fasta" name="output" metadata_source="input" /> |
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27 </outputs> |
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28 <tests> |
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29 <test> |
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30 <!-- Re-format a FASTA file into a single line --> |
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31 <param name="input" value="fasta_formatter1.fasta" /> |
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32 <param name="width" value="0" /> |
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33 <output name="output" file="fasta_formatter1.out" /> |
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34 </test> |
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35 <test> |
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36 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> |
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37 <param name="input" value="fasta_formatter1.fasta" /> |
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38 <param name="width" value="60" /> |
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39 <output name="output" file="fasta_formatter2.out" /> |
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40 </test> |
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41 </tests> |
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42 <help> |
0 | 43 **What it does** |
44 | |
45 This tool re-formats a FASTA file, changing the width of the nucleotides lines. | |
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46 |
0 | 47 **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. |
48 | |
49 -------- | |
50 | |
51 **Example** | |
52 | |
53 Input FASTA file (each nucleotides line is 50 characters long):: | |
54 | |
55 >Scaffold3648 | |
56 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC | |
57 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG | |
58 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA | |
59 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT | |
60 >Scaffold9299 | |
61 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG | |
62 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG | |
63 aactggtctttacctTTAAGTTG | |
64 | |
65 | |
66 Output FASTA file (with width=80):: | |
67 | |
68 >Scaffold3648 | |
69 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT | |
70 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA | |
71 ATTTTAATGAACATGTAGTAAAAACT | |
72 >Scaffold9299 | |
73 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC | |
74 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG | |
75 | |
76 Output FASTA file (with width=0 => single line):: | |
77 | |
78 >Scaffold3648 | |
79 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT | |
80 >Scaffold9299 | |
81 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG | |
82 | |
83 ------ | |
84 | |
85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
86 | |
87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
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88 </help> |
0 | 89 </tool> |