<tool id="commet" name="commet" version="24.7.14">
  <description>COmpare Multiple METagenomes</description>
  <requirements>
    <requirement type="package" version="24.7.14">commet</requirement>
    <requirement type="package" version="3.1.2">R</requirement>
  </requirements>
<command interpreter="python">
commet.py
#for $set in $sets
    --set ${set.setname}::${set.reads}
#end for
-k $kmer
-t $minsharedkmer
-l $minlengthread
-e $minshannonindex
#if str( $options_advanced.options_advanced_selector ) == "advanced"
-m $options_advanced.maxreads
-n $options_advanced.maxn
#end if
--output_vectors $output_vectors
--output_dendro $output_dendro
--output_matrix $output_matrix
--output_logs $output_logs
--output_heatmap1 $output_heatmap1
--output_heatmap2 $output_heatmap2
--output_heatmap3 $output_heatmap3
</command>

  <inputs>
	<!-- Input data files -->
        <repeat name="sets" title="Read sets" min="1">
            <param name="reads" type="data" multiple="true" format="fasta, fastq, fastq.gz" label="Dataset" help="Accept fasta/fastq/fastq.gz"/>
            <param name="setname" type="text" label="Set name" value="set_name" help="Please don't use spaces or special characters"/>
        </repeat>
	<param name="kmer" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
	<param name="minsharedkmer" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
	<param name="minlengthread" type="integer" label="Read mini length" value="0" help="Minimal length a read should have to be kept." />
	<param name="minshannonindex" type="float" label="Mini Shannon index" value="0" help="Minimal Shannon index a read should have to be kept. Float in [0,2.32]" />
	<conditional name="options_advanced">
		<param name="options_advanced_selector" type="select" label="Reads filter options" help="by default, all reads are kept with no Ns limitation">
			<option value="default" selected="true">default</option>
			<option value="advanced">advanced</option>
		</param>
		<when value="advanced">
			<param name="maxreads" type="integer" value="600" label="Maximum number of selected reads in sets" help="Maximum number of selected reads in sets. If a set is composed by 3 read files, and this option = 600, then the first 200 reads from each read file will be treated" />
			<param name="maxn" type="integer" value="5" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept." />
		</when>
	</conditional>
  </inputs>
  <outputs>
      <data format="zip" name="output_vectors" label="${tool.name} on ${on_string}: vector.zip" />
      <data format="zip" name="output_logs" label="${tool.name} on ${on_string}: logs.zip" />
      <data format="png" name="output_dendro" label="${tool.name} on ${on_string}: dendrogram.png" />
      <data format="zip" name="output_matrix" label="${tool.name} on ${on_string}: matrix.zip" />
      <data format="png" name="output_heatmap1" label="${tool.name} on ${on_string}: heatmap_normalized.png" />
      <data format="png" name="output_heatmap2" label="${tool.name} on ${on_string}: heatmap_percentage.png" />
      <data format="png" name="output_heatmap3" label="${tool.name} on ${on_string}: heatmap_plain.png" />
  </outputs>
  <stdio>
    <exit_code range="1" level="fatal" description="Error in Commet execution" />
  </stdio>  
  <help>

**Description**

COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.

Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation of read files, that can be used to further combine read subsets by common logical operations. Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps.


-------

**Web site**

http://colibread.inria.fr/commet/

-------

**Integrated by**

Yvan Le Bras and Cyril Monjeaud 

GenOuest Bio-informatics Core Facility

UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)

support@genouest.org

If you use this tool in Galaxy, please cite :

`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_


  </help>
<citations>
<citation type="doi">10.1186/1471-2105-13-S19-S10</citation>
<citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
    author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
    title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
    booktitle = {JOBIM 2013 Proceedings},
    year = {2013},
    url = {https://www.e-biogenouest.org/resources/128},
    pages = {97-106}
    }
</citation>
</citations>

</tool>