Mercurial > repos > konradpaszkiewicz > assemblystats
comparison 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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| -1:000000000000 | 0:6544228ea290 |
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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 <command interpreter="python"> | |
| 4 assembly_stats_txt.py | |
| 5 '$type' '$stats.extra_files_path' | |
| 6 '$type' | |
| 7 '$bucket' | |
| 8 '$input' | |
| 9 '$stats' | |
| 10 '$sortedcontigs' | |
| 11 '$histogrampng' | |
| 12 '$summedcontigspng' | |
| 13 '$histogramdata' | |
| 14 '$summedcontigdata' | |
| 15 | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <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)"> | |
| 19 <option value="contig" selected="yes">Contig (if from genomic assembly)</option> | |
| 20 <option value="isotig">Isotig (if from transcriptomic assembly)</option> | |
| 21 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option> | |
| 22 | |
| 23 </param> | |
| 24 <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"/> | |
| 25 <param format="fasta" name="input" type="data" label="Source file in FASTA format"/> | |
| 26 | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="tabular" name="stats" label="Assembly statistics"/> | |
| 30 <data format="fasta" name="sortedcontigs" label="Sorted contigs" /> | |
| 31 <data format="png" name="histogrampng" label="Histogram of contig sizes"/> | |
| 32 <data format="png" name="summedcontigspng" label="Cumulative sum of contig sizes"/> | |
| 33 <data format="tabular" name="histogramdata" label="Histogram data"/> | |
| 34 <data format="tabular" name="summedcontigdata" label="Cumulative sum of contig size data"/> | |
| 35 </outputs> | |
| 36 <requirements> | |
| 37 </requirements> | |
| 38 <help> | |
| 39 **Summarise assembly overview** | |
| 40 | |
| 41 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. | |
| 42 | |
| 43 | |
| 44 # Gives back | |
| 45 # - N50 | |
| 46 # - num of contigs > 1 kb | |
| 47 # - num of contigs | |
| 48 # - Read or Contig Histogram and graphs. | |
| 49 # - Summed contig length (by number of contigs, in sorted order) | |
| 50 </help> | |
| 51 | |
| 52 </tool> |