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annotate blobplot.xml @ 4:f35d462f57b9

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author Eduardo <eduardoalves@abdn.ac.uk>
date Wed, 25 Nov 2015 13:39:32 +0000
parents 0101d7d1211f
children dfa4f03b5baa
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Eduardo <eduardoalves@abdn.ac.uk>
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1 <tool id="blobplot" name="Blobplot" version="0.0.1">
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2 <description> Creates a plot of GC vs coverage for sequences colored by taxonomy</description>
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3 <requirements>
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4 <requirement type="package" version="0.9.3">r_ggplot2</requirement>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
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6
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7 </requirements>
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8 <command>
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9 cut -f1,13 $blast_res | perl gc_cov_annotate.pl --blasttaxid - --assembly $coding_seq --taxdump $TAXDUMP --bam $bam_file --out blob_file &amp;&amp;
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10 Rscript makeblobplot.R blob_file $ignore_below $tax_level &amp;&amp;
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11 mv blob_file.${tax_level}.png $output
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12 </command>
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13 <stdio>
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14 <exit_code range="1:" level="fatal" description="Tool exception" />
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15 </stdio>
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16 <inputs>
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17
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18 <param format="tabular" name="blast_res" type="data" label="Blast Results"/>
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19 <param format="fasta" name="coding_seq" type="data" label="Predicted Nucleotide Sequences"/>
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20 <param format="bam" name="bam_file" type="data" label="Aligned reads against Predicted Sequences"/>
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21 <param name="ignore_below" type="text" value="0.01" label="Cut off for plot"/>
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22 <param name="tax_level" type="select" label="Taxon level">
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23 <option value="taxlevel_superkingdom">Super Kingdom</option>
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24 <option value="taxlevel_phylum" selected="true">Phylum</option>
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25 <option value="taxlevel_order" >Order</option>
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26 <option value="taxlevel_species" >Species</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data format="png" name="output" label="${tool.name} on ${on_string} " />
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31 </outputs>
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32 <help>
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33 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.
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34
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35 Wrapper for Blobology developped by Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh
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36
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37 Contact Eduardo Alves at eduardoalves@abdn.ac.uk for support and bug reports.
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38 </help>
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39 </tool>
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40