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comparison twobittofa.xml @ 0:d025a40bbff1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
author iuc
date Fri, 19 Aug 2016 06:30:41 -0400
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children 4a81db403bd9
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-1:000000000000 0:d025a40bbff1
1 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@">
2 <macros>
3 <token name="@WRAPPER_VERSION@">332</token>
4 </macros>
5
6 <description>Convert all or part of .2bit file to fasta</description>
7
8 <requirements>
9 <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement>
10 </requirements>
11
12 <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command>
13
14 <command>
15 <![CDATA[
16 twoBitToFa
17 '$twobit_input'
18 '$fasta_output'
19
20 #if $seq
21 -seq='$seq'
22 #end if
23
24 #if $start
25 -start=$start
26 #end if
27
28 #if $end
29 -end=$end
30 #end if
31
32 #if $seqList
33 -seqList='$seqList'
34 #end if
35
36 $noMask
37 ]]>
38 </command>
39
40 <inputs>
41 <param name="twobit_input" type="data" format="twobit"
42 label="Input TwoBit file" help=""/>
43
44 <param argument="-seq" type="text" label="Restrict this to just one sequence
45 (Optional)" help="" optional="True"/>
46
47 <param argument="-start" type="integer" label="Start at given position in
48 sequence (Optional)" help="Zero-based" optional="True"/>
49
50 <param argument="-end" type="integer" label="End at given position in
51 sequence (Optional)" help="Non-inclusive" optional="True"/>
52
53 <param argument="-seqList" type="data" format="txt"
54 label="File containing list of the desired sequence names (Optional)"
55 help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
56 where coordinates are half-open zero-based, i.e. [start,end)"
57 optional="True"/>
58
59 <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue=""
60 checked="false" label="Convert sequence to all upper case?" help=""/>
61 </inputs>
62
63 <outputs>
64 <data format="fasta" name="fasta_output"/>
65 </outputs>
66
67 <tests>
68 <test>
69 <param name="twobit_input" value="input.2bit"/>
70 <output name="fasta_output" file="output.fasta" />
71 </test>
72 </tests>
73
74 <help><![CDATA[
75 **What it does**
76
77 twoBitToFa is a tool to convert all or part of .2bit file to fasta.
78
79 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html/>`_.
80
81 ]]></help>
82
83 <citations>
84 </citations>
85 </tool>