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annotate fsd.xml @ 45:6651e76baca1 draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty
author mheinzl
date Tue, 27 Aug 2019 07:36:53 -0400
parents a76af7fd9fca
children 901827154779
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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="1.0.6">
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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}' $log_axis $rel_freq --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 <param name="log_axis" type="boolean" label="log scale for y axis?" truevalue="" falsevalue="--log_axis" checked="False" help="Transform y axis in log scale."/>
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21 <param name="rel_freq" type="boolean" label="relative frequency?" truevalue="" falsevalue="--rel_freq" checked="False" help="If True, the relative frequencies instead of the absolute values are displayed in the plots."/>
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22 </inputs>
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23 <outputs>
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24 <data name="output_pdf" format="pdf" />
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25 <data name="output_tabular" format="tabular"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="file1" value="fsd_data1.tab"/>
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30 <param name="file2" value="fsd_data2.tab"/>
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31 <param name="file3" value="fsd_data3.tab"/>
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32 <param name="file4" value="fsd_data4.tab"/>
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33 <output name="output_pdf" file="fsd_output1.pdf" lines_diff="285"/>
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34 <output name="output_tabular" file="fsd_output1.tab"/>
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35 </test>
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36 <test>
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37 <param name="file1" value="fsd_data1.tab"/>
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38 <param name="file2" value="fsd_data2.tab"/>
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39 <param name="file3" value="fsd_data3.tab"/>
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40 <output name="output_pdf" file="fsd_output2.pdf" lines_diff="285"/>
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41 <output name="output_tabular" file="fsd_output2.tab"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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46 **What it does**
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47
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48 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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49
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50 ------
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52 **Input**
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53
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54 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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55
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56 1 AAAAAAAAAAAATGTTGGAATCTT ba
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57 10 AAAAAAAAAAAGGCGGTCCACCCC ab
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58 28 AAAAAAAAAAATGGTATGGACCGA ab
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59
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60 **Output**
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61
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62 The output is a PDF file with the plot and a tabular file with the data of the plot.
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63
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64 **About Author**
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65
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66 Author: Monika Heinzl
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67 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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68 Contact: monika.heinzl@edumail.at
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69
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70 ]]>
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71 </help>
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72 <citations>
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73 <citation type="bibtex">
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74 @misc{duplex,
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75 author = {Heinzl, Monika},
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76 year = {2018},
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77 title = {Development of algorithms for the analysis of duplex sequencing data}
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78 }
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79 </citation>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
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80 </citations>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
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81 </tool>