Mercurial > repos > ylebras > commet_docker
changeset 0:10dc665d6b03 default tip
first commit
author | ylebras |
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date | Wed, 18 Nov 2015 14:12:15 +0000 |
parents | |
children | |
files | commet.xml |
diffstat | 1 files changed, 108 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commet.xml Wed Nov 18 14:12:15 2015 +0000 @@ -0,0 +1,108 @@ +<tool id="commet_docker" name="commet" version="24.7.14"> + <description>COmpare Multiple METagenomes</description> + <requirements> + <container type="docker">ylebras/commet_galaxy</container> + </requirements> +<command > +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. <https://www.e-biogenouest.org/resources/128>`_ + + + </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> +