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annotate concoct.xml @ 2:bd409bbd287f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
author iuc
date Fri, 01 Jul 2022 14:10:59 +0000
parents 1f4286d836a3
children 4338452cbfb9
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bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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1 <tool id="concoct" name="CONCOCT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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2 <description>metagenome binning</description>
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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7 <command detect_errors="exit_code"><![CDATA[
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8 #set pca_components_file_name = 'PCA_components_data_gt' + str($advanced.length_threshold) + '.csv'
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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9 #set pca_transformed_file_name = 'PCA_transformed_data_gt' + str($advanced.length_threshold) + '.csv'
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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10 #set clustering_file_name = 'clustering_gt' + str($advanced.length_threshold) + '.csv'
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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11
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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12 ## CONCOCT doesn't handle gzipped files.
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13 #if $composition_file.ext.endswith(".gz")
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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14 gunzip -c '$composition_file' > composition_file.fa &&
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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15 #else:
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16 ln -s '$composition_file' composition_file.fa &&
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17 #end if
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18
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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19 mkdir outdir &&
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20 concoct
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21 --coverage_file '$coverage_file'
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22 --composition_file composition_file.fa
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23 --clusters $advanced.clusters
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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24 --kmer_length $advanced.kmer_length
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25 --threads \${GALAXY_SLOTS:-4}
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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26 --length_threshold $advanced.length_threshold
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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27 --read_length $advanced.read_length
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28 --total_percentage_pca $advanced.total_percentage_pca
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29 --basename 'outdir/'
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30 --seed $advanced.seed
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31 --iterations $advanced.iterations
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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32 --epsilon $advanced.epsilon
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33 $advanced.no_cov_normalization
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34 $advanced.no_total_coverage
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35 --no_original_data
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36 $advanced.converge_out
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37
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38 ## Convert all CONCOCT .csv outputs to tabular.
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39 && sed 's/\("\([^"]*\)"\)\?,/\2\t/g' outdir/$pca_components_file_name > '$output_pca_components'
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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40 && sed 's/\("\([^"]*\)"\)\?,/\2\t/g' outdir/$pca_transformed_file_name > '$output_pca_transformed'
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41 && sed 's/\("\([^"]*\)"\)\?,/\2\t/g' outdir/$clustering_file_name > '$output_clustering'
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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42 #if str($advanced.output_process_log) == 'yes':
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43 && mv outdir/log.txt '$process_log'
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44 #end if
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45 ]]></command>
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46 <inputs>
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47 <param argument="--coverage_file" type="data" format="tabular" label="Tabular coverage file" help="Columns correspond to samples and rows to contigs"/>
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48 <param argument="--composition_file" type="data" format="fasta,fasta.gz" label="Fasta file" help="Used to calculate the kmer composition (the genomic signature) of each contig"/>
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49 <section name="advanced" title="Advanced options">
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50 <param argument="--clusters" type="integer" value="400" label="Maximum number of clusters for the Variational Gaussian Mixture Model algorithm"/>
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51 <param argument="--kmer_length" type="integer" value="4" label="Kmer length"/>
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52 <param argument="--length_threshold" type="integer" value="1000" label="Sequence length threshold" help="Contigs shorter than this value will not be included"/>
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53 <param argument="--read_length" type="integer" value="100" label="Read length for coverage"/>
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54 <param argument="--total_percentage_pca" type="integer" value="100" label="Percentage of variance explained by the principal components for the combined data"/>
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55 <param argument="--seed" type="integer" min="0" value="1" label="Integer to use as seed for clustering" help="Zero value will use random seed"/>
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56 <param argument="--iterations" type="integer" value="500" label="Maximum number of iterations for the Variational Bayes Gaussian Mixture Models"/>
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57 <param argument="--epsilon" type="float" value="0.000001" label="Epsilon for the Variational Gaussian Mixture Model algorithm"/>
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58 <param argument="--no_cov_normalization" type="boolean" truevalue="--no_cov_normalization" falsevalue="" checked="false" label="Skip normalization and only do log transorm of the coverage?" help="By default, the coverage is normalized for samples, then normalized for contigs and finally log transformed"/>
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59 <param argument="--no_total_coverage" type="boolean" truevalue="--no_total_coverage" falsevalue="" checked="false" label="Eliminate the total coverage column from the coverage data matrix?" help="By default, total coverage is included, independently of coverage normalization but previous to log transformation"/>
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60 <param argument="--converge_out" type="boolean" truevalue="--converge_out" falsevalue="" checked="false" label="Output convergence information?"/>
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61 <param name="output_process_log" type="select" label="Output process log file?">
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62 <option value="no" selected="true">No</option>
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63 <option value="yes">Yes</option>
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64 </param>
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
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69 <filter>advanced['output_process_log'] == 'yes'</filter>
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70 </data>
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71 <data name="output_pca_components" format="tabular" label="${tool.name} on ${on_string} (PCA components)"/>
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72 <data name="output_pca_transformed" format="tabular" label="${tool.name} on ${on_string} (PCA transformed)"/>
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73 <data name="output_clustering" format="tabular" label="${tool.name} on ${on_string} (Clusters)"/>
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74 </outputs>
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75 <tests>
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76 <test expect_num_outputs="4">
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77 <param name="coverage_file" value="input1.tabular" ftype="tabular"/>
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78 <param name="composition_file" value="input1.fa.gz" ftype="fasta.gz"/>
bf23c688912a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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79 <param name="output_process_log" value="yes"/>
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bd409bbd287f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
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80 <output name="process_log" file="process_log.txt" ftype="txt" compare="re_match"/>
0
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81 <output name="output_pca_components" ftype="tabular">
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82 <assert_contents>
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83 <has_size value="367636"/>
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84 <has_text text="7377051e-02"/>
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85 </assert_contents>
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86 </output>
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87 <output name="output_pca_transformed" ftype="tabular">
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88 <assert_contents>
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89 <has_size value="737926"/>
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90 <has_text text="NODE_103_length_20202_cov_8.395357.0"/>
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91 </assert_contents>
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92 </output>
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93 <output name="output_clustering" ftype="tabular">
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94 <assert_contents>
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95 <has_size value="12167"/>
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96 <has_text text="NODE_103_length_20202_cov_8.395357"/>
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97 </assert_contents>
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98 </output>
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99 </test>
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100 </tests>
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101 <help><![CDATA[
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102 **What it does**
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103
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104 CONCOCT (Clustering cONtigs with COverage and ComposiTion) performs unsupervised binning of metagenomic contigs by
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105 using nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately
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106 (up to species level) bin metagenomic contigs.
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107
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108 The tool accepts 2 inputs; a tabular file where each row corresponds to a contig and each column corresponds to a
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109 sample (the values are the average coverage for this contig in that sample) and a file containing sequences in
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110 fasta format.
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111
1
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112 Three outputs are produced; clustering of the > 1000 kmer count, the PCA transformed matrix and the PCA components.
0
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113
1
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114 @HELP_OVERVIEW@
0
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115 ]]></help>
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116 <expand macro="citations"/>
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117 </tool>