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comparison assembly_stats_txt.xml @ 0:44c401ebc424 draft

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author aaronpetkau
date Sat, 04 Jul 2015 08:57:35 -0400
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1 <tool id="assemblystats" name="assemblystats" version="1.0.2">
2 <description>Summarise an assembly (e.g. N50 metrics)</description>
3 <requirements>
4 </requirements>
5 <command interpreter="python">
6 assembly_stats_txt.py
7 '$input_type' '$stats.extra_files_path'
8 '$input_type'
9 '$bucket'
10 '$input'
11 '$stats'
12 '$sortedcontigs'
13 '$histogrampng'
14 '$summedcontigspng'
15 '$histogramdata'
16 '$summedcontigdata'
17
18 </command>
19 <inputs>
20 <param help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)" label="Type of read" name="input_type" type="select">
21 <option selected="yes" value="contig">Contig (if from genomic assembly)</option>
22 <option value="isotig">Isotig (if from transcriptomic assembly)</option>
23 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
24 </param>
25 <param falsevalue="" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms" label="Output histogram with bin sizes=1" name="bucket" truevalue="-b" type="boolean" />
26 <param format="fasta" label="Source file in FASTA format" name="input" type="data" />
27 <param checked="false" help="If checked, all output files will be displayed. If not checked, only the file 'Assembly Statistics' will be provided." label="Return all output files" name="all_outputs" type="boolean" />
28 </inputs>
29 <outputs>
30 <data format="tabular" label="Assembly statistics - $input.display_name" name="stats" />
31 <data format="fasta" label="Sorted contigs - $input.display_name" name="sortedcontigs">
32 <filter>all_outputs is True</filter>
33 </data>
34 <data format="png" label="Histogram of contig sizes - $input.display_name" name="histogrampng">
35 <filter>all_outputs is True</filter>
36 </data>
37 <data format="png" label="Cumulative sum of contig sizes - $input.display_name" name="summedcontigspng">
38 <filter>all_outputs is True</filter>
39 </data>
40 <data format="tabular" label="Histogram data - $input.display_name" name="histogramdata">
41 <filter>all_outputs is True</filter>
42 </data>
43 <data format="tabular" label="Cumulative sum of contig size data - $input.display_name" name="summedcontigdata">
44 <filter>all_outputs is True</filter>
45 </data>
46 </outputs>
47 <help>
48 **Summarise assembly overview**
49
50 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.
51
52
53 # Gives back
54 # - N50
55 # - num of contigs &gt; 1 kb
56 # - num of contigs
57 # - Read or Contig Histogram and graphs.
58 # - Summed contig length (by number of contigs, in sorted order)
59 </help>
60 </tool>