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annotate tn93.xml @ 2:b38f620a3628 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
author iuc
date Wed, 20 Apr 2022 16:59:49 +0000
parents ccebde0e2d61
children 2fd21f5b16bc
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b38f620a3628 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
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1 <tool id="tn93" name="TN93" version="@TOOL_VERSION@+galaxy1">
0
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2 <description>compute distances between aligned sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
b38f620a3628 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
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6 <expand macro="requirements" />
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7 <version_command><![CDATA[tn93 --version]]></version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 tn93
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10 -o '$tn93_distances'
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11 #if str($options.advanced) == 'advanced':
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12 -t $options.threshold
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13 -a $options.ambigs
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14 -g $options.fraction
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15 -f csv
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16 -l $options.overlap
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17 #if $options.counts_in_name:
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18 -d '$options.counts_in_name'
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19 #end if
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20 #end if
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21 #if $second_fasta:
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22 -s '$second_fasta'
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23 #end if
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24 '$input_fasta'
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25 ]]></command>
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26 <inputs>
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27 <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
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28 <param name="second_fasta" argument="-s" type="data" format="fasta" optional="true"
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29 label="Additional input FASTA for pairwise comparisons" />
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30 <conditional name="options">
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31 <param label="Additional options" name="advanced" type="select">
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32 <option value="defaults">Use defaults</option>
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33 <option value="advanced">Specify additional parameters</option>
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34 </param>
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35 <when value="defaults" />
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36 <when value="advanced">
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37 <param name="threshold" type="float" value="0.015" min="0" max="1" label="Only report distances below this threshold" />
0
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38 <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
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39 <option value="handle">handle</option>
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40 <option value="resolve">resolve</option>
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41 <option value="average">average</option>
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42 <option value="skip">skip</option>
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43 <option value="gapmm">gapmm</option>
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44 </param>
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45 <param name="fraction" argument="-g" type="float" value="1.0"
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46 label="Maximum tolerated fraction of ambiguous characters" />
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47 <param name="overlap" argument="-l" type="integer" value="100"
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48 label="Only count pairs that overlap by at least N bases" />
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49 <param name="counts_in_name" argument="-d" type="text"
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50 optional="true" label="Sequence name component immediately preceding a copy number" />
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51 </when>
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52 </conditional>
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53 </inputs>
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54 <outputs>
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55 <data format="csv" name="tn93_distances" />
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="input_fasta" value="tn93-in1.fa" />
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60 <param name="advanced" value="advanced" />
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61 <param name="threshold" value="0.35" />
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62 <output file="tn93-out1.csv" ftype="csv" name="tn93_distances" sort="True" />
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63 </test>
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64 <test>
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65 <param name="input_fasta" value="tn93-in2-alpha.fa" />
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66 <param name="second_fasta" value="tn93-in2-beta.fa" />
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67 <param name="advanced" value="advanced" />
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68 <param name="threshold" value="0.35" />
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69 <output file="tn93-out2.csv" ftype="csv" name="tn93_distances" sort="True" />
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 TN93
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74 ----
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75
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76 Compute pairwise distances between aligned
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77 nucleotide sequences in sequential FASTA format using the
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78 [Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).
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79
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80 NOTES
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81 -----
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82
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83 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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84
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85 >seqname:10
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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86
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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87 ':' 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
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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88 only affect histogram and mean calculations.
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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89 ]]></help>
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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90 <expand macro="citations">
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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91 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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92 </expand>
ccebde0e2d61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
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93 </tool>