annotate assembly_stats_txt.xml @ 0:6544228ea290 default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

<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>