Mercurial > repos > devteam > fasta_formatter
comparison fasta_formatter.xml @ 3:859422bcb689 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
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date | Tue, 08 May 2018 13:25:51 -0400 |
parents | 9457a20156db |
children | 516b97a23d7e |
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2:9457a20156db | 3:859422bcb689 |
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1 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> | 1 <tool id="cshl_fasta_formatter" version="1.0.1" name="FASTA Width"> |
2 <description>formatter</description> | 2 <description>formatter</description> |
3 <requirements> | 3 <macros> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <import>macros.xml</import> |
5 </requirements> | 5 </macros> |
6 <expand macro="requirements" /> | |
6 <!-- | 7 <!-- |
7 Note: | 8 Note: |
8 fasta_formatter also has a tabular output mode (-t), | 9 fasta_formatter also has a tabular output mode (-t), |
9 but Galaxy already contains such a tool, so no need | 10 but Galaxy already contains such a tool, so no need |
10 to offer the user a duplicated tool. | 11 to offer the user a duplicated tool. |
11 | 12 |
12 So this XML tool only changes the width (line-wrapping) of a | 13 So this XML tool only changes the width (line-wrapping) of a |
13 FASTA file. | 14 FASTA file. |
14 --> | 15 --> |
15 <command> | 16 <command detect_errors="exit_code"><![CDATA[ |
16 <![CDATA[ | 17 @CATS@ fasta_formatter |
17 zcat -f < '$input' | fasta_formatter -w $width -o '$output' | 18 -w $width |
18 ]]> | 19 -o '$output' |
19 </command> | 20 ]]></command> |
20 <inputs> | 21 <inputs> |
21 <param format="fasta" name="input" type="data" label="Library to re-format" /> | 22 <expand macro="fasta_input" /> |
22 | 23 |
23 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> | 24 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> |
24 </inputs> | 25 </inputs> |
25 <outputs> | 26 <outputs> |
26 <data format="fasta" name="output" metadata_source="input" /> | 27 <data name="output" format="fasta" metadata_source="input" /> |
27 </outputs> | 28 </outputs> |
28 <tests> | 29 <tests> |
29 <test> | 30 <test> |
30 <!-- Re-format a FASTA file into a single line --> | 31 <!-- Re-format a FASTA file into a single line --> |
31 <param name="input" value="fasta_formatter1.fasta" /> | 32 <param name="input" value="fasta_formatter1.fasta" /> |
37 <param name="input" value="fasta_formatter1.fasta" /> | 38 <param name="input" value="fasta_formatter1.fasta" /> |
38 <param name="width" value="60" /> | 39 <param name="width" value="60" /> |
39 <output name="output" file="fasta_formatter2.out" /> | 40 <output name="output" file="fasta_formatter2.out" /> |
40 </test> | 41 </test> |
41 </tests> | 42 </tests> |
42 <help> | 43 <help><![CDATA[ |
43 **What it does** | 44 **What it does** |
44 | 45 |
45 This tool re-formats a FASTA file, changing the width of the nucleotides lines. | 46 This tool re-formats a FASTA file, changing the width of the nucleotides lines. |
46 | 47 |
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 **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. |
83 ------ | 84 ------ |
84 | 85 |
85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
86 | 87 |
87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
88 </help> | 89 ]]></help> |
90 <expand macro="citations" /> | |
89 </tool> | 91 </tool> |