Mercurial > repos > konradpaszkiewicz > assemblystats
view assembly_stats_txt.xml @ 0:6544228ea290 default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 16:24:46 -0400 |
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<tool id="assemblystats" name="assemblystats" version="1.0.1"> <description>Summarise an assembly (e.g. N50 metrics)</description> <command interpreter="python"> assembly_stats_txt.py '$type' '$stats.extra_files_path' '$type' '$bucket' '$input' '$stats' '$sortedcontigs' '$histogrampng' '$summedcontigspng' '$histogramdata' '$summedcontigdata' </command> <inputs> <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)"> <option value="contig" selected="yes">Contig (if from genomic assembly)</option> <option value="isotig">Isotig (if from transcriptomic assembly)</option> <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option> </param> <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"/> <param format="fasta" name="input" type="data" label="Source file in FASTA format"/> </inputs> <outputs> <data format="tabular" name="stats" label="Assembly statistics"/> <data format="fasta" name="sortedcontigs" label="Sorted contigs" /> <data format="png" name="histogrampng" label="Histogram of contig sizes"/> <data format="png" name="summedcontigspng" label="Cumulative sum of contig sizes"/> <data format="tabular" name="histogramdata" label="Histogram data"/> <data format="tabular" name="summedcontigdata" label="Cumulative sum of contig size data"/> </outputs> <requirements> </requirements> <help> **Summarise assembly overview** 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. # Gives back # - N50 # - num of contigs > 1 kb # - num of contigs # - Read or Contig Histogram and graphs. # - Summed contig length (by number of contigs, in sorted order) </help> </tool>