Mercurial > repos > devteam > fasta_formatter
comparison fasta_formatter.xml @ 2:9457a20156db draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Mon, 12 Oct 2015 10:15:31 -0400 |
parents | 1dbb5181c327 |
children | 859422bcb689 |
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1:1dbb5181c327 | 2:9457a20156db |
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1 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> | 1 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> |
2 <description>formatter</description> | 2 <description>formatter</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> |
5 </requirements> | 5 </requirements> |
6 <!-- | 6 <!-- |
7 Note: | 7 Note: |
8 fasta_formatter also has a tabular output mode (-t), | 8 fasta_formatter also has a tabular output mode (-t), |
9 but Galaxy already contains such a tool, so no need | 9 but Galaxy already contains such a tool, so no need |
10 to offer the user a duplicated tool. | 10 to offer the user a duplicated tool. |
11 | 11 |
12 So this XML tool only changes the width (line-wrapping) of a | 12 So this XML tool only changes the width (line-wrapping) of a |
13 FASTA file. | 13 FASTA file. |
14 --> | 14 --> |
15 <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command> | 15 <command> |
16 <inputs> | 16 <![CDATA[ |
17 <param format="fasta" name="input" type="data" label="Library to re-format" /> | 17 zcat -f < '$input' | fasta_formatter -w $width -o '$output' |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param format="fasta" name="input" type="data" label="Library to re-format" /> | |
18 | 22 |
19 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> | 23 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> |
20 </inputs> | 24 </inputs> |
21 | 25 <outputs> |
22 <tests> | 26 <data format="fasta" name="output" metadata_source="input" /> |
23 <test> | 27 </outputs> |
24 <!-- Re-format a FASTA file into a single line --> | 28 <tests> |
25 <param name="input" value="fasta_formatter1.fasta" /> | 29 <test> |
26 <param name="width" value="0" /> | 30 <!-- Re-format a FASTA file into a single line --> |
27 <param name="output" file="fasta_formatter1.out" /> | 31 <param name="input" value="fasta_formatter1.fasta" /> |
28 </test> | 32 <param name="width" value="0" /> |
29 <test> | 33 <output name="output" file="fasta_formatter1.out" /> |
30 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> | 34 </test> |
31 <param name="input" value="fasta_formatter1.fasta" /> | 35 <test> |
32 <param name="width" value="60" /> | 36 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> |
33 <param name="output" file="fasta_formatter2.out" /> | 37 <param name="input" value="fasta_formatter1.fasta" /> |
34 </test> | 38 <param name="width" value="60" /> |
35 </tests> | 39 <output name="output" file="fasta_formatter2.out" /> |
36 | 40 </test> |
37 <outputs> | 41 </tests> |
38 <data format="input" name="output" metadata_source="input" /> | 42 <help> |
39 </outputs> | |
40 | |
41 <help> | |
42 **What it does** | 43 **What it does** |
43 | 44 |
44 This tool re-formats a FASTA file, changing the width of the nucleotides lines. | 45 This tool re-formats a FASTA file, changing the width of the nucleotides lines. |
45 | 46 |
46 **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. | 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. |
47 | 48 |
48 -------- | 49 -------- |
49 | 50 |
50 **Example** | 51 **Example** |
82 ------ | 83 ------ |
83 | 84 |
84 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
85 | 86 |
86 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
87 | 88 </help> |
88 </help> | |
89 </tool> | 89 </tool> |