Mercurial > repos > eduardo > blobplot
annotate blobplot.xml @ 5:dfa4f03b5baa
added <requirement type="set_environment">
| author | Eduardo <eduardoalves@abdn.ac.uk> |
|---|---|
| date | Wed, 25 Nov 2015 13:54:48 +0000 |
| parents | 0101d7d1211f |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="blobplot" name="Blobplot" version="0.0.1"> |
| 2 <description> Creates a plot of GC vs coverage for sequences colored by taxonomy</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.9.3">r_ggplot2</requirement> | |
| 5 <requirement type="package" version="0.1.19">samtools</requirement> | |
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dfa4f03b5baa
added <requirement type="set_environment">
Eduardo <eduardoalves@abdn.ac.uk>
parents:
0
diff
changeset
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6 <requirement type="set_environment">TAXDUMP</requirement> |
| 0 | 7 </requirements> |
| 8 <command> | |
| 9 cut -f1,13 $blast_res | perl gc_cov_annotate.pl --blasttaxid - --assembly $coding_seq --taxdump $TAXDUMP --bam $bam_file --out blob_file && | |
| 10 Rscript makeblobplot.R blob_file $ignore_below $tax_level && | |
| 11 mv blob_file.${tax_level}.png $output | |
| 12 </command> | |
| 13 <stdio> | |
| 14 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 15 </stdio> | |
| 16 <inputs> | |
| 17 | |
| 18 <param format="tabular" name="blast_res" type="data" label="Blast Results"/> | |
| 19 <param format="fasta" name="coding_seq" type="data" label="Predicted Nucleotide Sequences"/> | |
| 20 <param format="bam" name="bam_file" type="data" label="Aligned reads against Predicted Sequences"/> | |
| 21 <param name="ignore_below" type="text" value="0.01" label="Cut off for plot"/> | |
| 22 <param name="tax_level" type="select" label="Taxon level"> | |
| 23 <option value="taxlevel_superkingdom">Super Kingdom</option> | |
| 24 <option value="taxlevel_phylum" selected="true">Phylum</option> | |
| 25 <option value="taxlevel_order" >Order</option> | |
| 26 <option value="taxlevel_species" >Species</option> | |
| 27 </param> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data format="png" name="output" label="${tool.name} on ${on_string} " /> | |
| 31 </outputs> | |
| 32 <help> | |
| 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. | |
| 34 | |
| 35 Wrapper for Blobology developped by Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh | |
| 36 | |
| 37 Contact Eduardo Alves at eduardoalves@abdn.ac.uk for support and bug reports. | |
| 38 </help> | |
| 39 </tool> | |
| 40 |