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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit edbe0509294e5c23c26cdae659ce5cf3ff69c363
author mheinzl
date Fri, 07 Dec 2018 07:23:07 -0500
parents fa3ff1c5280d
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="fsd_regions" name="FSD regions" version="1.0.1">
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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 <requirement type="package" version="0.15">pysam</requirement>
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8 </requirements>
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9 <command>
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10 python2 '$__tool_directory__/fsd_regions.py' --inputFile '$file1' --inputName1 '$file1.name' --bamFile '$file2' --rangesFile '$file3' --output_pdf $output_pdf --output_tabular $output_tabular
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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 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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14 <param name="file2" type="data" format="bam" label="Dataset 2: BAM file of aligned reads." help="Input in BAM format with the reads that were aligned to the reference genome."/>
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15 <param name="file3" type="data" format="bed" label="Dataset 3: BED file with chromsome, start and stop positions of regions." optional="true" help="BED file with start and stop positions of regions."/>
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16 </inputs>
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17 <outputs>
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18 <data name="output_pdf" format="pdf" />
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19 <data name="output_tabular" format="tabular"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="file1" value="fsd_reg.tab"/>
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24 <param name="file2" value="fsd_reg.bam"/>
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25 <param name="file3" value="fsd_reg_ranges.bed"/>
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26 <output name="output_pdf" file="fsd_reg_output.pdf" lines_diff="136"/>
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27 <output name="output_tabular" file="fsd_reg_output.tab"/>
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28 </test>
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29 </tests>
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30 <help> <![CDATA[
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32 **What it does**
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33
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34 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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37 **Input**
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38
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39 **Dataset 1:** 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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41 1 AAAAAAAAAAAATGTTGGAATCTT ba
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42 10 AAAAAAAAAAAGGCGGTCCACCCC ab
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43 28 AAAAAAAAAAATGGTATGGACCGA ab
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44
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45 **Dataset 2:** BAM file of the aligned reads. This file can be obtained by the tool "Map with BWA-MEM".
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46
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47 **Dataset 3 (optional):** BED file with start and stop positions of the regions. If it is not provided, then all aligned reads of the BAM file are used in the distribution of family sizes::
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49 ACH_TDII 90 633
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50 ACH_TDII 659 1140
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51 ACH_TDII 1144 1561
0
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53 **Output**
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54
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55 The output is a PDF file with the plot and a tabular file with the data of the plot.
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58 **About Author**
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60 Author: Monika Heinzl
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61
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62 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
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63
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64 Contact: monika.heinzl@edumail.at
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65
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66 ]]>
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67
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68 </help>
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69 <citations>
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70 <citation type="bibtex">
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71 @misc{duplex,
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72 author = {Heinzl, Monika},
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73 year = {2018},
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74 title = {Development of algorithms for the analysis of duplex sequencing data}
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75 }
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76 </citation>
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77 </citations>
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78 </tool>