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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 4c46f2914e9da5c310feb886b64fca8eb09ea767
author mheinzl
date Wed, 23 May 2018 15:06:27 -0400
parents 2631864873d7
children b202c97deabe
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="fsd_regions" name="Duplex Sequencing Analysis: fsd_regions" version="0.0.4">
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
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5 <requirement type="package" version="1.4">matplotlib</requirement>
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6 </requirements>
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7 <description>Family size distribution (FSD) of user-specified regions</description>
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8 <command>
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9 python2 $__tool_directory__/fsd_regions.py --inputFile "$file1" --inputName1 "$file1.name" --ref_genome "$file2" --sep $separator --output_pdf $output_pdf --output_csv $output_csv
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10 </command>
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11 <inputs>
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12 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags of whole dataset" optional="false" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family."/>
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13 <param name="file2" type="data" format="txt" label="Dataset 2: input tags aligned to the reference genome" help="Input in txt format with the regions and the tags, which were aligned to the reference genome."/>
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14 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
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15 </inputs>
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16 <outputs>
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17 <data name="output_pdf" format="pdf" />
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18 <data name="output_csv" format="csv"/>
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19 </outputs>
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20 <help> <![CDATA[
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22 **What it does**
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24 This tool will create a distribution of family sizes of all tags, which were aligned to the reference genome. The distribution is separated after the regions of the reference genome.
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27 **Input**
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29 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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31 +-----+----------------------------+----+
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32 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba |
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33 +-----+----------------------------+----+
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34 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |
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35 +-----+----------------------------+----+
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36 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
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37 +-----+----------------------------+----+
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38
1
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40 In addition, a TXT file with the regions and all tags that were aligned to the reference genome is required. This file can obtained from a different tool.
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42 +-----------+------------------------------+
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43 | 87_636 | AAATCAAAGTATGAATGAAGTTGCCT |
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44 +-----------+------------------------------+
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45 | 87_636 | AAATTCATAGCATTAATTTCAACGGG |
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46 +-----------+------------------------------+
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47 | 656_1143 | GGGGCAGCCATATTGGCAATTATCAT |
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48 +-----------+------------------------------+
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50 **Output**
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52 The output is a PDF file with the plot and a CSV with the data of the plot.
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55 **About Author**
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57 Author: Monika Heinzl
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59 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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61 Contact: monika.heinzl@edumail.at
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63 ]]>
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64
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65 </help>
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66 <citations>
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67 <citation type="bibtex">
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68 @misc{duplex,
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69 author = {Heinzl, Monika},
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70 year = {2018},
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71 title = {Development of algorithms for the analysis of duplex sequencing data}
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72 }
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73 </citation>
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74 </citations>
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75 </tool>