view blobplot.xml @ 6:b45fc20c7acd

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<tool id="blobplot" name="Blobplot" version="0.0.1">
  <description> Creates a plot of GC vs coverage for sequences colored by taxonomy</description>
  <requirements>
      <requirement type="package" version="0.9.3">r_ggplot2</requirement>
      <requirement type="package" version="0.1.19">samtools</requirement>
      <requirement type="set_environment">TAXDUMP</requirement>
  </requirements>
  <command>
  cut -f1,13 $blast_res | perl gc_cov_annotate.pl --blasttaxid -  --assembly $coding_seq --taxdump $TAXDUMP --bam $bam_file --out  blob_file  &amp;&amp;
  Rscript  makeblobplot.R blob_file $ignore_below $tax_level &amp;&amp;
 mv  blob_file.${tax_level}.png $output
  </command>
  <stdio>
    <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <inputs>

    <param format="tabular" name="blast_res" type="data" label="Blast Results"/>
    <param format="fasta" name="coding_seq" type="data" label="Predicted Nucleotide Sequences"/>
    <param format="bam" name="bam_file" type="data" label="Aligned reads against Predicted Sequences"/>
    <param name="ignore_below" type="text" value="0.01" label="Cut off for plot"/>
    <param  name="tax_level" type="select" label="Taxon level">
 	<option value="taxlevel_superkingdom">Super Kingdom</option>
	<option value="taxlevel_phylum" selected="true">Phylum</option>
	<option value="taxlevel_order" >Order</option>
	<option value="taxlevel_species" >Species</option>
	</param>
  </inputs> 
  <outputs> 
      <data format="png" name="output" label="${tool.name} on ${on_string} " />
  </outputs>
  <help>
	This tool creates a GC vs Coverage plot coloured by taxonomic id for a set of sequences given blast results annotated with tax id and aligments of reads against the sequences.

Wrapper for Blobology developped by Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh

    Contact Eduardo Alves at [e-mail] for support and bug reports.
  </help>
</tool>