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comparison fasta_formatter.xml @ 2:61469a8970cd draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:39:03 -0400
parents 2cbdd2fc365b
children 4f66158f20f2
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1:2cbdd2fc365b 2:61469a8970cd
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 <output 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 <output 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>