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annotate fsd.xml @ 7:43b16247c35a draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 0641c8994fa786f303f6546d88ce24f15504d9b0
author mheinzl
date Wed, 09 May 2018 09:24:18 -0400
parents c4b8222dce29
children 7d5c86d59850
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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="Duplex Sequencing Analysis:" version="0.0.8">
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4 <description>Family size distribution (FSD) of tags</description>
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5 <requirements>
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6 <requirement type="package" version="1.4">matplotlib</requirement>
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7 </requirements>
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9 <command>
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10 python $__tool_directory__/fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_csv $output_csv --output_pdf $output_pdf
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11 </command>
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12 <inputs>
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13 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
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14 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" />
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15 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
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16 <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, blanks are not allowed!"/>
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17 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
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18 </inputs>
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19 <outputs>
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20 <data name="output_pdf" format="pdf" />
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21 <data name="output_csv" format="csv"/>
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22 </outputs>
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23 <!-- <tests>
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24 <test>
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25 <param name="file1" value="Test_data.tabular"/>
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26 <param name="file2" value="None"/>
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27 <param name="file3" value="None"/>
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28 <param name="file4" value="None"/>
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29 <output name="output_pdf" file="output_file.pdf"/>
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30 <output name="output_csv" file="output_file.csv"/>
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31 </test>
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32 </tests>
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33 -->
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34 <help> <![CDATA[
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36 **What it does**
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38 This tool will create a distribution of family sizes of each tag, which is separated after families 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. If multiple files are provided as input, the family size distribution without separation contains all datasets in one plot and for each dataset a distribution with separation after single ab, ba strands and DCSs is produced.
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41 **Input**
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43 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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45 **!!! Name of the files can have max. 34 charcters, blanks are not allowed !!!**
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47 +-----+----------------------------+----+
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48 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba |
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49 +-----+----------------------------+----+
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50 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |
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51 +-----+----------------------------+----+
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52 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
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53 +-----+----------------------------+----+
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59 **Output**
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61 The output is a PDF file with the plot and a CSV with the data of the plot.
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64 **About Author**
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66 Author: Monika Heinzl
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68 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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70 Contact: monika.heinzl@edumail.at
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72 ]]>
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74 </help>
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75 <citations>
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76 <citation type="bibtex">
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77 @misc{duplex,
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78 author = {Heinzl, Monika},
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79 year = {2018},
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80 title = {Development of algorithms for the analysis of duplex sequencing data}
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81 }
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
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82 </citation>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
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83 </citations>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
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84 </tool>