Mercurial > repos > iuc > msaboot

annotate msaboot.xml @ 2:5892ac21ab6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit caa5b2ebe69a901746f84fe24460d73282d3a773
author iuc
date Tue, 06 Mar 2018 17:44:39 -0500
parents 9625ddf6eed5
children 99f8b4e631e5
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48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
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1 <?xml version="1.0"?>
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
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2 <tool id="msaboot" name="MSABOOT" version="@VERSION@">
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3 <description>Output PHYLIP file with bootstrapped multiple sequence alignment data</description>
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4 <macros>
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5 <token name="@VERSION@">0.1.1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">msaboot</requirement>
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9 </requirements>
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10 <version_command>msaboot --version</version_command>
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11 <command detect_errors="aggressive">
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12 <![CDATA[
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13 msaboot -i '$input' -n $number -o '$output'
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14 #if $save_logfile:
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15 > '$log' 2>&1
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16 #end if
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input" format="fasta" type="data" label="FASTA input file" />
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21 <param name="number" type="integer" value="1" min="1" label="Specify the number of bootstrapping replicates to generate." />
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22 <param name="save_logfile" type="boolean" truevalue="" falsevalue="" label="Output log file" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="phylip" label="${tool.name} on ${on_string}:out.phylip" />
48b414c7d38e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e
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26 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_msabootpl_run.txt">
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27 <filter>save_logfile</filter>
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28 </data>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input" value="msa.fasta" />
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33 <param name="number" value="10" />
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34 <param name="save_logfile" value="true" />
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35 <output name="log" file="log.txt" ftype="txt" compare="contains" />
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36 <output name="output" file="out.phylip" ftype="phylip" compare="contains" />
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37 </test>
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38 </tests>
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39 <help>
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40 <![CDATA[
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41
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42 ===========
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43 Description
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44 ===========
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45
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46 .. class:: infomark
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47
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48 A tool for creating bootstrapping replicates from Multiple Sequence Alignment data.
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49
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50 .. _msaboot: https://github.com/phac-nml/msaboot
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51
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52 -----
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53
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54 -----
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55 Input
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56 -----
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57 Input file location of FASTA file containing Multiple Sequence Alignment data(-i)
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58
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59 ----------
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60 Parameters
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61 ----------
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62 Number of bootstrapping replicates (-n)
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63
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64 ------
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65 Output
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66 ------
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67
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68 This tool produces two output files, one of which is optional (the log file).
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69
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70 (A) The bootstrapped replicates in Phylip format.
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71
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72 (B) The optional log file, containing information about the msaboot run to bootstrap the multiple sequence alignment data.
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73
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74 ]]>
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75 </help>
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76 <citations>
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77 <citation type="bibtex">
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78 @misc{GitHubmsaboot,
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79 title = {msaboot},
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80 publisher = {phac-nml},
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81 journal = {GitHub repository},
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82 url = {https://github.com/phac-nml/msaboot},
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83 }
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84 </citation>
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85 </citations>
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86 </tool>