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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 8833d1a8a49d7b6d4a9c849b0335d3260564b351-dirty
author mheinzl
date Tue, 20 Nov 2018 09:51:47 -0500
parents b202c97deabe
children eabfdc012d7b
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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="1.0.0">
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3 <description>Family size distribution (FSD) of user-specified regions in the reference genome</description>
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4 <requirements>
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package" version="1.4.0">matplotlib</requirement>
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7 </requirements>
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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' --output_pdf $output_pdf --output_tabular $output_tabular
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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 in the reference genome and the tags, which were aligned to the reference genome."/>
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14 </inputs>
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15 <outputs>
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16 <data name="output_pdf" format="pdf" />
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17 <data name="output_tabular" format="tabular"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="file1" value="Test_data.tabular"/>
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22 <param name="file2" value="Test_data_regions.txt"/>
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23 <output name="output_pdf" file="output_file.pdf" lines_diff="136"/>
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24 <output name="output_tabular" file="output_file.tabular"/>
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25 </test>
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26 </tests>
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27 <help> <![CDATA[
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29 **What it does**
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31 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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34 **Input**
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36 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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38 +-----+----------------------------+----+
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39 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba |
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40 +-----+----------------------------+----+
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41 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |
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42 +-----+----------------------------+----+
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43 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
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44 +-----+----------------------------+----+
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45
1
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47 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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49 +-----------+------------------------------+
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50 | 87_636 | AAATCAAAGTATGAATGAAGTTGCCT |
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51 +-----------+------------------------------+
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52 | 87_636 | AAATTCATAGCATTAATTTCAACGGG |
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53 +-----------+------------------------------+
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54 | 656_1143 | GGGGCAGCCATATTGGCAATTATCAT |
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55 +-----------+------------------------------+
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57 **Output**
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58
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59 The output is a PDF file with the plot and a tabular file with the data of the plot.
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62 **About Author**
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64 Author: Monika Heinzl
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65
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66 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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67
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68 Contact: monika.heinzl@edumail.at
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70 ]]>
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72 </help>
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73 <citations>
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74 <citation type="bibtex">
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75 @misc{duplex,
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76 author = {Heinzl, Monika},
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77 year = {2018},
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78 title = {Development of algorithms for the analysis of duplex sequencing data}
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79 }
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80 </citation>
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81 </citations>
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82 </tool>