Mercurial > repos > jay > pdaug_sequence_similarity_network
annotate PDAUG_Sequence_Network/PDAUG_Sequence_Network.xml @ 5:9012052b1dad draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:00:07 +0000 |
parents | e650de82bcc7 |
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e650de82bcc7
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 <tool id="pdaug_sequence_similarity_network" name="PDAUG Sequence Similarity Network" version="0.1.0" python_template_version="3.6"> |
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2 <description>Generates a sequence similarity network</description> |
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3 |
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4 <requirements> |
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5 <requirement type="package" version="0.12.0">python-Levenshtein</requirement> |
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6 <requirement type="package" version="3.2.2">matplotlib</requirement> |
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7 <requirement type="package" version="2.5">networkx</requirement> |
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8 </requirements> |
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9 |
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10 <command detect_errors="exit_code"><![CDATA[ |
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11 |
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12 python '$__tool_directory__/PDAUG_Sequence_Network.py' --InFile '$input1' --OutFile 'out.png' |
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13 ]]></command> |
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14 |
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15 <inputs> |
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16 <param name="input1" type="data" format="fasta" label="Input fasta file" argument= "--InFile" help="Input fasta file with peptides"/> |
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17 |
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18 </inputs> |
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20 <outputs> |
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21 <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png" /> |
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22 |
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23 </outputs> |
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24 |
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25 <tests> |
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26 <test> |
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27 <param name="input1" value="positive.fasta"/> |
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28 <output name="output2" file="out.png" compare="sim_size" delta="10000" /> |
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29 </test> |
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30 </tests> |
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31 |
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32 <help><![CDATA[ |
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33 .. class:: infomark |
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34 |
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35 **What it does** |
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36 |
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37 This tool calculates Levenshtein distance between peptide sequences and plots the data in the form of a sequence similarity network. |
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38 |
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39 ----- |
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40 |
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41 **Inputs** |
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42 * **--InFile** Takes peptide sequences as fasta file. |
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43 |
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44 ----- |
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45 |
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46 **Outputs** |
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47 * Return html report file.]]></help> |
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48 <citations> |
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49 <citation type="bibtex"> |
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50 @misc{PDAUGGITHUB, |
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51 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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52 year = {2020}, |
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53 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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54 publisher = {GitHub}, |
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55 journal = {GitHub repository}, |
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56 url = |
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57 {https://github.com/jaidevjoshi83/pdaug.git}, |
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58 } |
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59 </citation> |
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60 </citations> |
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61 </tool> |
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