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comparison fasta_formatter.xml @ 3:4f66158f20f2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:33:30 -0400
parents 61469a8970cd
children 381e98a18f01
comparison
equal deleted inserted replaced
2:61469a8970cd 3:4f66158f20f2
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>