diff blobplot.xml @ 0:0101d7d1211f

initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blobplot.xml	Wed Nov 25 11:26:59 2015 +0000
@@ -0,0 +1,40 @@
+<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>
+
+  </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>
+