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annotate fsd.xml @ 16:6bd9ef49d013 draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
author mheinzl
date Mon, 08 Oct 2018 05:50:18 -0400
parents 32921a67437b
children 2e517a54eedc
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!-- galaxy version 16.04 -->
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3 <tool id="fsd" name="FSD" version="1.0.0">
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4 <description>: Family Size Distribution of duplex sequencing tags</description>
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5 <requirements>
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6 <requirement type="package" version="2.7">python</requirement>
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7 <requirement type="package" version="1.4.0">matplotlib</requirement>
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8 </requirements>
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10 <command>
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11 python2 '$__tool_directory__/fsd.py' --inputFile1 '${file1}' --inputName1 '${file1.name}'
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12 --inputFile2 '${file2}' --inputName2 '${file2.name}' --inputFile3 '${file3}' --inputName3 '${file3.name}'
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13 --inputFile4 '${file4}' --inputName4 '${file4.name}' --output_pdf $output_pdf --output_tabular $output_tabular
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14 </command>
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15 <inputs>
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16 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
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17 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" />
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18 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
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19 <param name="file4" type="data" format="tabular" label="Dataset 4: input tags" optional="true" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family. Name of the files can have max. 34 charcters!"/>
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20 </inputs>
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21 <outputs>
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22 <data name="output_pdf" format="pdf" />
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23 <data name="output_tabular" format="tabular"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="file1" value="Test_data.tabular"/>
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28 <param name="file2" value="Test_data2.tabular"/>
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29 <param name="file3" value="Test_data3.tabular"/>
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30 <param name="file4" value="Test_data4.tabular"/>
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31 <output name="output_pdf" file="output_file.pdf" lines_diff="285"/>
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32 <output name="output_tabular" file="output_file.tabular"/>
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33 </test>
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34 <test>
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35 <param name="file1" value="Test_data.tabular"/>
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36 <param name="file2" value="Test_data2.tabular"/>
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37 <param name="file3" value="Test_data3.tabular"/>
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38 <output name="output_pdf" file="output_file2.pdf" lines_diff="285"/>
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39 <output name="output_tabular" file="output_file2.tabular"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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44 **What it does**
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45
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46 This tool will create a distribution of family sizes of each tag, which is separated after tags that have only the forward (ab) strand, the reverse (ba) strand or both strands (ab+ba) of the DCS and a family size distribution without separation is created.
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47
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48 ------
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49
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50 **Input**
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51
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52 This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands::
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53
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54 1 AAAAAAAAAAAATGTTGGAATCTT ba
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55 10 AAAAAAAAAAAGGCGGTCCACCCC ab
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56 28 AAAAAAAAAAATGGTATGGACCGA ab
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57
0
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58 **Output**
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59
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60 The output is a PDF file with the plot and a tabular file with the data of the plot.
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61
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62 **About Author**
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63
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64 Author: Monika Heinzl
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65 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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66 Contact: monika.heinzl@edumail.at
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67
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68 ]]>
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69 </help>
0
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70 <citations>
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71 <citation type="bibtex">
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72 @misc{duplex,
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73 author = {Heinzl, Monika},
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74 year = {2018},
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75 title = {Development of algorithms for the analysis of duplex sequencing data}
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76 }
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77 </citation>
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78 </citations>
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79 </tool>