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comparison assembly_stats_txt.xml @ 0:ad2b274663f8 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
author nml
date Tue, 07 Nov 2017 12:28:31 -0500
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1 <tool id="assemblystats" name="assemblystats" version="1.0.1">
2 <description>Summarise an assembly (e.g. N50 metrics)</description>
3 <requirements>
4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
5 <requirement type="package" version="5.0.4">gnuplot</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 python $__tool_directory__/assembly_stats_txt.py
9
10 '$type'
11 '$stats.extra_files_path'
12 '$type'
13 '$bucket'
14 '$input'
15 '$stats'
16 '$sortedcontigs'
17 '$histogrampng'
18 '$summedcontigspng'
19 '$histogramdata'
20 '$summedcontigdata'
21 ]]></command>
22 <inputs>
23 <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)">
24 <option value="contig" selected="yes">Contig (if from genomic assembly)</option>
25 <option value="isotig">Isotig (if from transcriptomic assembly)</option>
26 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
27 </param>
28 <param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="-b" falsevalue="" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/>
29 <param format="fasta" name="input" type="data" label="Source file in FASTA format"/>
30 <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." />
31 </inputs>
32 <outputs>
33 <data format="tabular" name="stats" label="Assembly statistics - $input.display_name"/>
34 <data format="fasta" name="sortedcontigs" label="Sorted contigs - $input.display_name" >
35 <filter>all_outputs is True</filter>
36 </data>
37 <data format="png" name="histogrampng" label="Histogram of contig sizes - $input.display_name">
38 <filter>all_outputs is True</filter>
39 </data>
40 <data format="png" name="summedcontigspng" label="Cumulative sum of contig sizes - $input.display_name">
41 <filter>all_outputs is True</filter>
42 </data>
43 <data format="tabular" name="histogramdata" label="Histogram data - $input.display_name">
44 <filter>all_outputs is True</filter>
45 </data>
46 <data format="tabular" name="summedcontigdata" label="Cumulative sum of contig size data - $input.display_name">
47 <filter>all_outputs is True</filter>
48 </data>
49 </outputs>
50 <tests>
51 <test>
52 <param name="input" value="SRR1002850_SMALL.fasta"/>
53 <output name="stats" value="Assembly_statistics_-_SRR1002850_SMALL.fasta.tabular"/>
54 </test>
55 </tests>
56 <help><![CDATA[
57 **Summarise assembly overview**
58
59 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.
60
61
62 # Gives back
63 # - N50
64 # - num of contigs > 1 kb
65 # - num of contigs
66 # - Read or Contig Histogram and graphs.
67 # - Summed contig length (by number of contigs, in sorted order)
68 ]]>
69
70 </help>
71 <citations>
72 <citation type="bibtex">@ARTICLE{a1,
73 title = {Summarise an assembly (e.g. N50 metrics)},
74 author = {Konrad Paszkiewicz, Sujai Kumar, Mariam Iskander},
75 url = {https://github.com/phac-nml/galaxy_tools/}
76 }
77 }</citation>
78 </citations>
79 </tool>