Mercurial > repos > iuc > colibread_commet
view commet.xml @ 1:291753bf4013 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author | iuc |
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date | Fri, 24 Nov 2017 12:48:26 -0500 |
parents | 10e0e74c83af |
children | d03353742508 |
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<?xml version='1.0' encoding='utf-8'?> <tool profile="16.04" id="commet" name="Commet" version="24.7.14"> <description>COmpare Multiple METagenomes</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="24.7.14">commet</requirement> </requirements> <command><![CDATA[ #for $i, $set in enumerate( $sets ) echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt && #end for Commet.py -k ${k} -t ${t} -l ${l} -e ${e} #if str( $options_advanced.options_advanced_selector ) == "advanced" -m ${options_advanced.m} -n ${options_advanced.n} #end if commet_input_sets.txt ]]></command> <inputs> <!-- Input data files --> <repeat name="sets" title="Read sets" min="1"> <param name="reads" type="data" multiple="true" format="fasta, fastq" label="Dataset" help="Accept fasta/fastq"/> </repeat> <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." /> <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." /> <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." /> <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." /> <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="default" /> <when value="advanced"> <param argument="-m" type="integer" value="-1" 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. (-1 = any)" /> <param argument="-n" type="integer" value="-1" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept. (-1 = all)" /> </when> </conditional> <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/> <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/> <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/> </inputs> <outputs> <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" > <filter>plain_outputs</filter> </data> <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" > <filter>percentage_outputs</filter> </data> <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" > <filter>normalized_outputs</filter> </data> <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" /> <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" > <filter>normalized_outputs</filter> </data> <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" > <filter>percentage_outputs</filter> </data> <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" > <filter>plain_outputs</filter> </data> </outputs> <tests> <test> <param name="input_type" value="list" /> <repeat name="sets"> <param name="reads" value="commet/A.fa" ftype="fasta" /> </repeat> <repeat name="sets"> <param name="reads" value="commet/B.fa,commet/C.fa" ftype="fasta" /> </repeat> <repeat name="sets"> <param name="reads" value="commet/D.fa" ftype="fasta" /> </repeat> <param name="plain_outputs" value="True"/> <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/> <output name="matrix_plain" file="commet/matrix_plain.csv"/> </test> </tests> <help><![CDATA[ **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/ ]]></help> <expand macro="citations"> <citation type="doi">10.1186/1471-2105-13-S19-S10</citation> </expand> </tool>