Mercurial > repos > iuc > kmer2stats

annotate kmer2stats.xml @ 1:6ae87ffcea01 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/kmer2stats/ commit 069a351be3e6272c2d511c545593f32fd18f8a84
author iuc
date Tue, 22 Apr 2025 11:34:36 +0000
parents a926baa751bf
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1 <tool id="kmer2stats" name="Kmer2Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>A tool that computes kmer alpha diversity metrics and other statistics</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.1</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">kmer2stats</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 kmer2stats.py
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13 '$input_file'
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14 &&
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15 cp 'compute_diversity.csv' '$output_file'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="input_file" type="data" format="tabular,txt" label="File input"/>
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20 </inputs>
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21 <outputs>
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22 <data name="output_file" format="tabular" label="${tool.name}: kmer statistics"/>
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23 </outputs>
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24 <tests>
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25 <test expect_num_outputs="1">
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26 <param name="input_file" ftype="txt" value="test_file.txt"/>
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27 <output name="output_file" ftype="tabular" value="compute_diversity.csv"/>
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28 </test>
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29 </tests>
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30 <help>
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31 <![CDATA[
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32
1
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33 **What this tool does**
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34
1
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35 This tool calculates alpha diversity metrics and other statistics such as observed features based on counted kmers.
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36
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37 **Input**
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38
1
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39 This tool was designed to use the output from jellyfish but it also can take any file that looks like this:
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41 ::
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42
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43 ANYTHING SINCE THIS LINE WILL ALWAYS BE SKIPPED
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44 AAAAAA 8453
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45 AAAAAC 6870
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46 AAAAAG 6312
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47 AAAAAT 7966
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48 AAAACA 5133
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49 AAAACC 5600
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50 AAAACG 5870
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51 AAAACT 3911
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52 AAAAGA 4173
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53 AAAAGC 5078
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54 AAAAGG 3047
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55 AAAAGT 3067
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56 AAAATA 5726
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57 AAAATC 6167
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58 AAAATG 5731
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59 AAAATT 4987
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60 AAACAA 3719
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61 AAACAC 2817
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62 AAACAG 5565
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63
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64 The first line will always be skipped so be sure to start the counted kmers in the second row!
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65
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66 **Output**
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67
1
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68 Two column table with metric name in the first column and value in second column.
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69
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70 ::
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71
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72 Metric Value
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73 shannon 3.0008343481203097
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74 simpson_d 0.05166872360281036
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75 pielou_e 0.9856502651904311
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76
0
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77 ]]>
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78 </help>
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79 <citations>
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80 <citation type="bibtex">@misc{BibEntry2025Apr,
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81 title = {{kmer2stats}},
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82 author = {Santino Faack (SantaMcCloud)},
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83 journal = {GitHub},
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84 year = {2025},
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85 month = apr,
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86 url = {https://github.com/SantaMcCloud/kmer2stats}
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87 }</citation>
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88 </citations>
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89 </tool>