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comparison msaboot.xml @ 0:48b414c7d38e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
author iuc
date Mon, 19 Feb 2018 14:07:33 -0500
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children 9625ddf6eed5
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-1:000000000000 0:48b414c7d38e
1 <?xml version="1.0"?>
2 <tool id="msaboot" name="MSABOOT" version="@VERSION@">
3 <description>Output PHYLIP file with bootstrapped multiple sequence alignment data</description>
4 <macros>
5 <token name="@VERSION@">0.1.0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@VERSION@">msaboot</requirement>
9 </requirements>
10 <version_command>msaboot --version</version_command>
11 <command detect_errors="aggressive">
12 <![CDATA[
13 msaboot -i '$input' -n $number -o '$output'
14 #if $save_logfile:
15 > '$log' 2>&1
16 #end if
17 ]]>
18 </command>
19 <inputs>
20 <param name="input" format="fasta" type="data" label="FASTA input file" />
21 <param name="number" type="integer" value="1" min="1" label="Specify the number of bootstrapping replicates to generate." />
22 <param name="save_logfile" type="boolean" truevalue="" falsevalue="" label="Output log file" />
23 </inputs>
24 <outputs>
25 <data name="output" format="phylip" label="${tool.name} on ${on_string}:out.phylip" />
26 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_msabootpl_run.txt">
27 <filter>save_logfile</filter>
28 </data>
29 </outputs>
30 <tests>
31 <test>
32 <param name="input" value="msa.fasta" />
33 <param name="number" value="10" />
34 <param name="save_logfile" value="true" />
35 <output name="log" file="log.txt" ftype="txt" compare="contains" />
36 <output name="output" file="out.phylip" ftype="phylip" compare="contains" />
37 </test>
38 </tests>
39 <help>
40 <![CDATA[
41
42 ===========
43 Description
44 ===========
45
46 .. class:: infomark
47
48 A tool for creating bootstrapping replicates from Multiple Sequence Alignment data.
49
50 .. _msaboot: https://github.com/phac-nml/msaboot
51
52 -----
53
54 -----
55 Input
56 -----
57 Input file location of FASTA file containing Multiple Sequence Alignment data(-i)
58
59 ----------
60 Parameters
61 ----------
62 Number of bootstrapping replicates (-n)
63
64 ------
65 Output
66 ------
67
68 This tool produces two output files, one of which is optional (the log file).
69
70 (A) The bootstrapped replicates in Phylip format.
71
72 (B) The optional log file, containing information about the msaboot run to bootstrap the multiple sequence alignment data.
73
74 ]]>
75 </help>
76 <citations>
77 <citation type="bibtex">
78 @misc{GitHubmsaboot,
79 title = {msaboot},
80 publisher = {phac-nml},
81 journal = {GitHub repository},
82 url = {https://github.com/phac-nml/msaboot},
83 }
84 </citation>
85 </citations>
86 </tool>