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annotate assembly_stats_txt.xml @ 1:7556309ffbaf draft default tip

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit fb4c29f720748f46ff501140f2cd306bab6614f9"
author nml
date Fri, 29 May 2020 13:51:50 -0400
parents ad2b274663f8
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1 <tool id="assemblystats" name="assemblystats" version="1.1.0">
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2 <description>Summarise an assembly (e.g. N50 metrics)</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
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5 <requirement type="package" version="5.2.7">gnuplot</requirement>
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6 <requirement type="package" version="3.7.6">python</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 python3 $__tool_directory__/assembly_stats_txt.py
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10
1
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11 -d '$stats.extra_files_path'
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12 -t '$type'
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13 -i '$input'
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14 -s '$stats'
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15 -sc '$sortedcontigs'
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16 -hpng '$histogrampng'
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17 -spng '$summedcontigspng'
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18 -hd '$histogramdata'
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19 -scd '$summedcontigdata'
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21 #if $bucket
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22 -b
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23 #end if
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24
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25 ]]></command>
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26 <inputs>
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27 <param label="Type of read" name="type" type="select" help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)">
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28 <option value="contig" selected="yes">Contig (if from genomic assembly)</option>
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29 <option value="isotig">Isotig (if from transcriptomic assembly)</option>
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30 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
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31 </param>
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32 <param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="true" falsevalue="false" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/>
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33 <param format="fasta" name="input" type="data" label="Source file in FASTA format"/>
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34 <param name = "all_outputs" type ="boolean" checked="false" label="Return all output files" help="If checked, all output files will be displayed. If not checked, only the file 'Assembly Statistics' will be provided." />
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35 </inputs>
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36 <outputs>
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37 <data format="tabular" name="stats" label="Assembly statistics - $input.display_name"/>
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38 <data format="fasta" name="sortedcontigs" label="Sorted contigs - $input.display_name" >
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39 <filter>all_outputs is True</filter>
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40 </data>
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41 <data format="png" name="histogrampng" label="Histogram of contig sizes - $input.display_name">
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42 <filter>all_outputs is True</filter>
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43 </data>
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44 <data format="png" name="summedcontigspng" label="Cumulative sum of contig sizes - $input.display_name">
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45 <filter>all_outputs is True</filter>
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46 </data>
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47 <data format="tabular" name="histogramdata" label="Histogram data - $input.display_name">
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48 <filter>all_outputs is True</filter>
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49 </data>
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50 <data format="tabular" name="summedcontigdata" label="Cumulative sum of contig size data - $input.display_name">
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51 <filter>all_outputs is True</filter>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input" value="SRR1002850_SMALL.fasta"/>
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57 <output name="stats" value="Assembly_statistics_-_SRR1002850_SMALL.fasta.tabular"/>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 **Summarise assembly overview**
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62
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63 This script is used to give summary statistics of an assembly or set of reads. Typically this is run after an assembly to evaluate gross features.
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64
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65
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66 # Gives back
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67 # - N50
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68 # - num of contigs > 1 kb
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69 # - num of contigs
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70 # - Read or Contig Histogram and graphs.
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71 # - Summed contig length (by number of contigs, in sorted order)
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72 ]]>
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73
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74 </help>
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75 <citations>
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76 <citation type="bibtex">@ARTICLE{a1,
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77 title = {Summarise an assembly (e.g. N50 metrics)},
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78 author = {Konrad Paszkiewicz, Sujai Kumar, Mariam Iskander},
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79 url = {https://github.com/phac-nml/galaxy_tools/}
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80 }
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81 }</citation>
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82 </citations>
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83 </tool>