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comparison twobittofa.xml @ 1:4a81db403bd9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
author iuc
date Wed, 13 Sep 2017 17:54:17 -0400
parents d025a40bbff1
children 356dc923f8d3
comparison
equal deleted inserted replaced
0:d025a40bbff1 1:4a81db403bd9
1 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@"> 1 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@">
2 <description>Convert all or part of .2bit file to FASTA</description>
2 <macros> 3 <macros>
3 <token name="@WRAPPER_VERSION@">332</token> 4 <token name="@WRAPPER_VERSION@">332</token>
4 </macros> 5 </macros>
5
6 <description>Convert all or part of .2bit file to fasta</description>
7
8 <requirements> 6 <requirements>
9 <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement> 7 <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement>
10 </requirements> 8 </requirements>
9 <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command>
10 <command><![CDATA[
11 twoBitToFa
12 '$twobit_input'
13 '$fasta_output'
11 14
12 <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command> 15 #if $seq
16 -seq='$seq'
17 #end if
13 18
14 <command> 19 #if str($start)
15 <![CDATA[ 20 -start=$start
16 twoBitToFa 21 #end if
17 '$twobit_input'
18 '$fasta_output'
19 22
20 #if $seq 23 #if str($end)
21 -seq='$seq' 24 -end=$end
22 #end if 25 #end if
23 26
24 #if $start 27 #if $seqList
25 -start=$start 28 -seqList='$seqList'
26 #end if 29 #end if
27 30
28 #if $end 31 $noMask
29 -end=$end 32 ]]></command>
30 #end if
31
32 #if $seqList
33 -seqList='$seqList'
34 #end if
35
36 $noMask
37 ]]>
38 </command>
39 33
40 <inputs> 34 <inputs>
41 <param name="twobit_input" type="data" format="twobit" 35 <param name="twobit_input" type="data" format="twobit" label="Input TwoBit file" />
42 label="Input TwoBit file" help=""/> 36 <param argument="-seq" type="text" optional="true" label="Restrict this to just one sequence" help="Optional" />
43 37 <param argument="-start" type="integer" optional="true" label="Start at given position in sequence" help="Zero-based, optional"/>
44 <param argument="-seq" type="text" label="Restrict this to just one sequence 38 <param argument="-end" type="integer" optional="true" label="End at given position in sequence" help="Non-inclusive, optional" />
45 (Optional)" help="" optional="True"/> 39 <param argument="-seqList" type="data" format="txt" 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)" 40 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 41 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)" 42 where coordinates are half-open zero-based, i.e. [start,end)" />
57 optional="True"/> 43 <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" checked="false" label="Convert sequence to all upper case?" />
58
59 <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue=""
60 checked="false" label="Convert sequence to all upper case?" help=""/>
61 </inputs> 44 </inputs>
62
63 <outputs> 45 <outputs>
64 <data format="fasta" name="fasta_output"/> 46 <data name="fasta_output" format="fasta" />
65 </outputs> 47 </outputs>
66
67 <tests> 48 <tests>
68 <test> 49 <test>
69 <param name="twobit_input" value="input.2bit"/> 50 <param name="twobit_input" value="input.2bit"/>
70 <output name="fasta_output" file="output.fasta" /> 51 <output name="fasta_output" file="output.fasta" />
71 </test> 52 </test>
72 </tests> 53 </tests>
73
74 <help><![CDATA[ 54 <help><![CDATA[
75 **What it does** 55 **What it does**
76 56
77 twoBitToFa is a tool to convert all or part of .2bit file to fasta. 57 twoBitToFa is a tool to convert all or part of .2bit file to FASTA.
78 58
79 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html/>`_. 59 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
80
81 ]]></help> 60 ]]></help>
82
83 <citations> 61 <citations>
84 </citations> 62 </citations>
85 </tool> 63 </tool>