Mercurial > repos > jay > pdaug_word_vector_model
annotate PDAUG_Word_Vector_Model/PDAUG_Word_Vector_Model.xml @ 0:3ce435b8d648 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:21:16 +0000 |
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children | c6a1b09d8846 |
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1 <tool id="pdaug_word_vector_model" name="PDAUG Word Vector Model" python_template_version="3.7" version="0.1.0"> |
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2 <description>Generates the skip-gram model</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.0.3">pandas</requirement> |
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5 <requirement type="package" version="1.76">biopython</requirement> |
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6 <requirement type="package" version="3.5">nltk</requirement> |
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7 <requirement type="package" version="3.8.0">gensim</requirement> |
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8 <requirement type="package" version="0.23.1">scikit-learn</requirement> |
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9 <requirement type="package" version="1.18.4">numpy</requirement> |
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10 </requirements> |
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11 <stdio> |
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12 <exit_code range="1" level="fatal" /> |
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13 </stdio> |
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14 <command detect_errors="exit_code"><![CDATA[ |
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15 |
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16 python '$__tool_directory__/PDAUG_Word_Vector_Model.py' -I '$input' -M '$meanCount' -W '$window' -O '$OutFile' |
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17 |
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18 ]]></command> |
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19 |
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20 <inputs> |
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21 <param name="input" type="data" label="Input fasta file" format="fasta" argument= "--Input" help="Input fasta file with peptides"/> |
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22 <param name="meanCount" type="integer" label="Mean Count" value="0" format="fasta" argument= "--min_count" help="Ignores a all words with total frequency lower than this"/> |
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23 <param name="window" type="integer" label="window" value="5" argument="--window" help="Maximum distance between the current and predicted word within a sentence"/> |
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24 </inputs> |
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25 |
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26 <outputs> |
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27 <data name='OutFile' format='txt' label="${tool.name} on $on_string - (text)" /> |
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28 </outputs> |
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29 |
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30 <tests> |
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31 <test> |
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32 <param name="input" value="test.fasta"/> |
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33 <param name="meanCount" value="0"/> |
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34 <param name="window" value="5"/> |
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35 <output name="OutFile" value="model.txt" lines_diff="2268" /> |
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36 </test> |
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37 </tests> |
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38 <help><![CDATA[ |
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39 .. class:: infomark |
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40 |
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41 **What it does** |
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42 |
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43 This tool calculates the skip-gram model which is a neural network where the inputs and outputs of the network are one-hot vectors calculated based on training data that contains input word and output word. |
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44 |
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45 ----- |
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46 |
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47 **Inputs** |
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48 * **--Input** Fasta file with protein sequences. |
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49 * **--min_count** Ignores all words with total frequency lower than this |
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50 * **--window** Maximum distance between the current and predicted word within a sentence, accepts integer value. |
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51 |
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52 ----- |
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53 |
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54 **Outputs** |
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55 * **--OutFile** Return "model.txt" model file. |
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56 |
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57 ]]></help> |
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58 |
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59 <citations> |
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60 |
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61 <citation type="bibtex"> |
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62 @misc{PDAUGGITHUB, |
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63 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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64 year = {2020}, |
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65 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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66 publisher = {GitHub}, |
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67 journal = {GitHub repository}, |
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68 url = |
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69 {https://github.com/jaidevjoshi83/pdaug.git}, |
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70 } |
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71 </citation> |
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72 |
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73 <citation type="bibtex"> |
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74 @inproceedings{rehurek_lrec, |
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75 title = {{Software Framework for Topic Modelling with Large Corpora}}, |
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76 author = {Radim {\v R}eh{\r u}{\v r}ek and Petr Sojka}, |
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77 booktitle = {{Proceedings of the LREC 2010 Workshop on New |
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78 Challenges for NLP Frameworks}}, |
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79 pages = {45--50}, |
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80 year = 2010, |
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81 month = May, |
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82 day = 22, |
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83 publisher = {ELRA}, |
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84 address = {Valletta, Malta}, |
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85 url={http://is.muni.cz/publication/884893/en}, |
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86 language={English} |
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87 } |
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88 </citation> |
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89 |
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90 <citation type="bibtex"> |
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91 @article{Md_Nafiz, |
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92 title= {Identifying antimicrobial peptides using word embedding with deep recurrent neural networks}, |
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93 volume={35}, |
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94 DOI={https://doi.org/10.1093/bioinformatics/bty937}, |
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95 issue={12}, |
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96 year={2018}, |
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97 pages={2009-2016}, |
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98 journal={Europe PMC}, |
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99 author={Hamid, Md-Nafiz and Friedberg, Iddo} |
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100 } |
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101 |
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102 </citation> |
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103 </citations> |
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104 </tool> |
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105 |
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106 |
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107 |