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comparison fasplit.xml @ 0:6ea5ae81aec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
author iuc
date Wed, 13 Sep 2017 17:53:19 -0400
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-1:000000000000 0:6ea5ae81aec1
1 <tool id="fasplit" name="faSplit" version="@WRAPPER_VERSION@">
2 <description>Split a FASTA file</description>
3 <macros>
4 <token name="@WRAPPER_VERSION@">332</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">ucsc-fasplit</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 mkdir out &&
11 faSplit
12 $O.split_type
13 '$input'
14 #if $O.split_type != 'byname'
15 $O.count
16 #end if
17 out/
18 ]]></command>
19 <inputs>
20 <param name="input" type="data" format="fasta" label="FASTA file" />
21 <conditional name="O">
22 <param name="split_type" type="select" label="Split by:">
23 <option value="sequence" selected="true">Number of files (for multi sequence FASTA)</option>
24 <option value="base">Number of files (for single sequence FASTA)</option>
25 <option value="size">Number of base (for single sequence FASTA)</option>
26 <option value="byname">By name</option>
27 </param>
28 <when value="sequence">
29 <param name="count" type="integer" value="10" label="Number of chunks" />
30 </when>
31 <when value="base">
32 <param name="count" type="integer" value="10" label="Number of chunks" />
33 </when>
34 <when value="size">
35 <param name="count" type="integer" value="100" label="Size of chunks (bp)" />
36 </when>
37 <when value="byname" />
38 </conditional>
39 </inputs>
40 <outputs>
41 <collection name="output_list" type="list" label="${tool.name} on ${on_string}">
42 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" ext="fasta" directory="out"/>
43 </collection>
44 </outputs>
45
46 <tests>
47 <test>
48 <param name="input" ftype="fasta" value="CDS.fa" />
49 <param name="split_type" value="sequence" />
50 <param name="count" value="5" />
51 <output_collection name="output_list" type="list">
52 <element name="0" file="0.fa" />
53 <element name="1" file="1.fa" />
54 <element name="2" file="2.fa" />
55 <element name="3" file="3.fa" />
56 <element name="4" file="4.fa" />
57 </output_collection>
58 </test>
59 <test>
60 <param name="input" ftype="fasta" value="CDS.fa"/>
61 <param name="split_type" value="byname"/>
62 <output_collection name="output_list" type="list">
63 <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" />
64 <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" />
65 <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" />
66 <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
67 <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" />
68 <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" />
69 <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
70 <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" />
71 <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" />
72 <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
73 <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" />
74 <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" />
75 <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
76 <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
77 <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" />
78 <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
79 <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
80 <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" />
81 <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
82 <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
83 <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" />
84 <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
85 <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
86 <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" />
87 <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
88 <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
89 <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" />
90 <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
91 <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
92 <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" />
93 <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
94 <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
95 <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" />
96 <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
97 <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
98 <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" />
99 <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
100 <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
101 <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" />
102 </output_collection>
103 </test>
104 </tests>
105 <help><![CDATA[
106 **What it does**
107
108 `faSplit`_ is a tool to split a single FASTA file into several files.
109
110 .. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
111 ]]></help>
112 <citations>
113 </citations>
114 </tool>