Mercurial > repos > cmonjeau > commet
view commet.xml @ 6:a53ce9294c0a
fix logs output
author | cmonjeau |
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date | Thu, 10 Sep 2015 14:40:43 +0000 |
parents | 8b2edb8a315e |
children | 9590778f5181 |
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<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="3.0.1">R_3_0_1</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. <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>