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annotate tn93.xml @ 1:0a4d18edbdd2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty
author dave
date Wed, 20 Mar 2019 13:04:30 -0400
parents 08f2130e39b3
children
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08f2130e39b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty
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1 <tool id="tn93" name="TN93" version="1.0.4">
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2 <description>compute distances between aligned sequences</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.4">tn93</requirement>
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5 </requirements>
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6 <version_command><![CDATA[tn93 --version]]></version_command>
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7 <command detect_errors="exit_code"><![CDATA[
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8 tn93
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9 -o '$tn93_distances'
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10 #if str($options.advanced) == 'advanced':
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11 -t $options.threshold
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12 -a $options.ambigs
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13 -g $options.fraction
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14 -f csv
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15 -l $options.overlap
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16 #if $options.counts_in_name:
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17 -d '$options.counts_in_name'
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18 #end if
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19 #end if
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20 #if $second_fasta:
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21 -s '$second_fasta'
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22 #end if
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23 '$input_fasta'
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24 ]]></command>
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25 <inputs>
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26 <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
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27 <param name="second_fasta" argument="-s" type="data" format="fasta" optional="true"
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28 label="Additional input FASTA for pairwise comparisons" />
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29 <conditional name="options">
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30 <param label="Additional options" name="advanced" type="select">
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31 <option value="defaults">Use defaults</option>
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32 <option value="advanced">Specify additional parameters</option>
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33 </param>
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34 <when value="defaults" />
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35 <when value="advanced">
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36 <param name="threshold" type="float" value="0.015" label="Only report distances below this threshold" />
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37 <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
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38 <option value="handle">handle</option>
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39 <option value="resolve">resolve</option>
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40 <option value="average">average</option>
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41 <option value="skip">skip</option>
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42 <option value="gapmm">gapmm</option>
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43 </param>
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44 <param name="fraction" argument="-g" type="float" value="1.0"
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45 label="Maximum tolerated fraction of ambiguous characters" />
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46 <param name="overlap" argument="-l" type="integer" value="100"
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47 label="Only count pairs that overlap by at least N bases" />
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48 <param name="counts_in_name" argument="-d" type="text"
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49 optional="true" label="Sequence name component immediately preceding a copy number" />
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50 </when>
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51 </conditional>
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52 </inputs>
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53 <outputs>
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54 <data format="csv" name="tn93_distances" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="input_fasta" value="tn93-in1.fa" />
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59 <param name="advanced" value="advanced" />
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60 <param name="threshold" value="0.35" />
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61 <output file="tn93-out1.csv" ftype="csv" name="tn93_distances" sort="True" />
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62 </test>
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63 <test>
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64 <param name="input_fasta" value="tn93-in2-alpha.fa" />
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65 <param name="second_fasta" value="tn93-in2-beta.fa" />
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66 <param name="advanced" value="advanced" />
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67 <param name="threshold" value="0.35" />
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68 <output file="tn93-out2.csv" ftype="csv" name="tn93_distances" sort="True" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 TN93
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73 ----
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74
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75 Compute pairwise distances between aligned
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76 nucleotide sequences in sequential FASTA format using the
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77 [Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).
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78
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79 NOTES
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80 -----
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81
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82 All sequences must be aligned and have the same length. Only IUPAC characters are recognized (e.g. no ~). Sequence names can include copy number as in
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83
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84 >seqname:10
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85
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86 ':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers
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87 only affect histogram and mean calculations.
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88 ]]></help>
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89 <citations>
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90 <citation type="bibtex">
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91 @UNPUBLISHED{spond,
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92 author = "Sergei Kosakovsky Pond",
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93 title = "HyPhy: Hypothesis Testing using Phylogenies",
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94 year = "2000",
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95 note = "http://hyphy.org/",
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96 url = "http://hyphy.org/"}
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97 </citation>
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98 </citations>
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99 </tool>