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annotate fsd.xml @ 10:f7136e93604b draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
author mheinzl
date Tue, 15 May 2018 13:49:34 -0400
parents 2c5fc522ded4
children b615c7e51f40
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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="0.0.11">
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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="2.7">python</requirement>
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7 <requirement type="package" version="1.4">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 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_pdf $output_pdf --output_csv $output_csv
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12 </command>
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13 <inputs>
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14 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
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15 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" />
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16 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
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17 <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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18 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
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19 </inputs>
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20 <outputs>
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21 <data name="output_pdf" format="pdf" />
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22 <data name="output_csv" format="csv"/>
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23 </outputs>
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24 <!-- <tests>
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25 <test>
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26 <param name="file1" value="Test_data.tabular"/>
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27 <param name="file2" value="None"/>
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28 <param name="file3" value="None"/>
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29 <param name="file4" value="None"/>
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30 <output name="output_pdf" file="output_file.pdf"/>
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31 <output name="output_csv" file="output_file.csv"/>
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32 </test>
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33 </tests>
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34 -->
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35 <help> <![CDATA[
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37 **What it does**
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39 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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42 **Input**
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44 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
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46 **!!! Name of the files can have max. 34 charcters !!!**
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48 +-----+----------------------------+----+
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49 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba |
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50 +-----+----------------------------+----+
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51 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |
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52 +-----+----------------------------+----+
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53 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
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54 +-----+----------------------------+----+
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60 **Output**
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62 The output is a PDF file with the plot and a CSV with the data of the plot.
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65 **About Author**
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67 Author: Monika Heinzl
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69 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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71 Contact: monika.heinzl@edumail.at
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73 ]]>
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75 </help>
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76 <citations>
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77 <citation type="bibtex">
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78 @misc{duplex,
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79 author = {Heinzl, Monika},
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80 year = {2018},
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81 title = {Development of algorithms for the analysis of duplex sequencing data}
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82 }
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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83 </citation>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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84 </citations>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
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85 </tool>