| Next changeset 1:031f84cb2fd3 (2022-03-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37" |
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added:
concoct.xml extract_fasta_bins.py macros.xml test-data/input1.fa.gz test-data/input1.tabular test-data/inputcluster1.tabular test-data/process_log.txt |
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| diff -r 000000000000 -r 06c0eb033025 concoct.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/concoct.xml Fri Feb 18 14:18:11 2022 +0000 |
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| @@ -0,0 +1,116 @@ +<tool id="concoct" name="CONCOCT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>metagenome binning</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#set pca_components_file_name = 'PCA_components_data_gt' + str($advanced.length_threshold) + '.csv' +#set pca_transformed_file_name = 'PCA_transformed_data_gt' + str($advanced.length_threshold) + '.csv' +#set clustering_file_name = 'clustering_gt' + str($advanced.length_threshold) + '.csv' + +## CONCOCT doesn't handle gzipped files. +#if $composition_file.ext.endswith(".gz") + gunzip -c '$composition_file' > composition_file.fa && +#else: + ln -s '$composition_file' composition_file.fa && +#end if + +mkdir outdir && +concoct +--coverage_file '$coverage_file' +--composition_file composition_file.fa +--clusters $advanced.clusters +--kmer_length $advanced.kmer_length +--threads \${GALAXY_SLOTS:-4} +--length_threshold $advanced.length_threshold +--read_length $advanced.read_length +--total_percentage_pca $advanced.total_percentage_pca +--basename 'outdir/' +--seed $advanced.seed +--iterations $advanced.iterations +--epsilon $advanced.epsilon +$advanced.no_cov_normalization +$advanced.no_total_coverage +--no_original_data +$advanced.converge_out + +## Convert all CONCOCT .csv outputs to tabular. +&& sed 's/\("\([^"]*\)"\)\?,/\2\t/g' outdir/$pca_components_file_name > '$output_pca_components' +&& sed 's/\("\([^"]*\)"\)\?,/\2\t/g' outdir/$pca_transformed_file_name > '$output_pca_transformed' +&& sed 's/\("\([^"]*\)"\)\?,/\2\t/g' outdir/$clustering_file_name > '$output_clustering' +#if str($advanced.output_process_log) == 'yes': + && mv outdir/log.txt '$process_log' +#end if + ]]></command> + <inputs> + <param argument="--coverage_file" type="data" format="tabular" label="Tabular coverage file" help="Columns correspond to samples and rows to contigs"/> + <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"/> + <section name="advanced" title="Advanced options"> + <param argument="--clusters" type="integer" value="400" label="Maximum number of clusters for the Variational Gaussian Mixture Model algorithm"/> + <param argument="--kmer_length" type="integer" value="4" label="Kmer length"/> + <param argument="--length_threshold" type="integer" value="1000" label="Sequence length threshold" help="Contigs shorter than this value will not be included"/> + <param argument="--read_length" type="integer" value="100" label="Read length for coverage"/> + <param argument="--total_percentage_pca" type="integer" value="100" label="Percentage of variance explained by the principal components for the combined data"/> + <param argument="--seed" type="integer" min="0" value="1" label="Integer to use as seed for clustering" help="Zero value will use random seed"/> + <param argument="--iterations" type="integer" value="500" label="Maximum number of iterations for the Variational Bayes Gaussian Mixture Models"/> + <param argument="--epsilon" type="float" value="0.000001" label="Epsilon for the Variational Gaussian Mixture Model algorithm"/> + <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"/> + <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"/> + <param argument="--converge_out" type="boolean" truevalue="--converge_out" falsevalue="" checked="false" label="Output convergence information?"/> + <param name="output_process_log" type="select" label="Output process log file?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + </section> + </inputs> + <outputs> + <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> + <filter>advanced['output_process_log'] == 'yes'</filter> + </data> + <data name="output_pca_components" format="tabular" label="${tool.name} on ${on_string} (PCA components)"/> + <data name="output_pca_transformed" format="tabular" label="${tool.name} on ${on_string} (PCA transformed)"/> + <data name="output_clustering" format="tabular" label="${tool.name} on ${on_string} (Clusters)"/> + </outputs> + <tests> + <test expect_num_outputs="4"> + <param name="coverage_file" value="input1.tabular" ftype="tabular"/> + <param name="composition_file" value="input1.fa.gz" ftype="fasta.gz"/> + <param name="output_process_log" value="yes"/> + <output name="process_log" file="process_log.txt" ftype="txt" compare="contains"/> + <output name="output_pca_components" ftype="tabular"> + <assert_contents> + <has_size value="367636"/> + <has_text text="7377051e-02"/> + </assert_contents> + </output> + <output name="output_pca_transformed" ftype="tabular"> + <assert_contents> + <has_size value="737926"/> + <has_text text="NODE_103_length_20202_cov_8.395357.0"/> + </assert_contents> + </output> + <output name="output_clustering" ftype="tabular"> + <assert_contents> + <has_size value="12167"/> + <has_text text="NODE_103_length_20202_cov_8.395357"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +CONCOCT (Clustering cONtigs with COverage and ComposiTion) performs unsupervised binning of metagenomic contigs by +using nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately +(up to species level) bin metagenomic contigs. + +The tool accepts 2 inputs; a tabular file where each row corresponds to a contig and each column corresponds to a +sample (the values are the average coverage for this contig in that sample) and a file containing sequences in +fasta format. + +Three are produced; clustering of the > 1000 kmer count, the PCA transformed matrix and the PCA components. + + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 06c0eb033025 extract_fasta_bins.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_fasta_bins.py Fri Feb 18 14:18:11 2022 +0000 |
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| @@ -0,0 +1,49 @@ +#!/usr/bin/env python + +import argparse +import gzip +import os +import sys +from collections import defaultdict +from functools import partial + +import pandas as pd +from Bio import SeqIO + +parser = argparse.ArgumentParser(description=__doc__) + +parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped') +parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Input Fasta file") +parser.add_argument("--input_cluster", action="store", dest="input_cluster", help="Concoct output cluster file") +parser.add_argument("--output_path", help="Output directory") + +args = parser.parse_args() + +all_seqs = {} +if args.gzipped: + _open = partial(gzip.open, mode='rt') +else: + _open = open + +with _open(args.input_fasta) as fh: + for seq in SeqIO.parse(fh, "fasta"): + all_seqs[seq.id] = seq + +# Make sure we're reading the file as tabular! +df = pd.read_csv(args.input_cluster, sep='\t') +try: + assert df.columns[0] == 'contig_id' + assert df.columns[1] == 'cluster_id' +except AssertionError: + sys.stderr.write("ERROR! Header line was not 'contig_id, cluster_id', please adjust your input file. Exiting!\n") + sys.exit(-1) + +cluster_to_contigs = defaultdict(list) +for i, row in df.iterrows(): + cluster_to_contigs[row['cluster_id']].append(row['contig_id']) + +for cluster_id, contig_ids in cluster_to_contigs.items(): + output_file = os.path.join(args.output_path, "{0}.fa".format(cluster_id)) + seqs = [all_seqs[contig_id] for contig_id in contig_ids] + with open(output_file, 'w') as ofh: + SeqIO.write(seqs, ofh, 'fasta') |
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| diff -r 000000000000 -r 06c0eb033025 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 18 14:18:11 2022 +0000 |
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| @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">concoct</requirement> + <requirement type="package" version="0.19.2">pandas</requirement> + <requirement type="package" version="1.79">biopython</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.3103</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 06c0eb033025 test-data/input1.fa.gz |
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| Binary file test-data/input1.fa.gz has changed |
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| diff -r 000000000000 -r 06c0eb033025 test-data/input1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.tabular Fri Feb 18 14:18:11 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r 06c0eb033025 test-data/inputcluster1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcluster1.tabular Fri Feb 18 14:18:11 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +contig_id cluster_id +NODE_1_length_2054_cov_17.474684 77 +NODE_2_length_16156_cov_8.219856 93 |
| b |
| diff -r 000000000000 -r 06c0eb033025 test-data/process_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/process_log.txt Fri Feb 18 14:18:11 2022 +0000 |
| b |
| @@ -0,0 +1,10 @@ +Results created at +Successfully loaded composition data. +Successfully loaded coverage data. +Performed PCA, resulted in 154 dimensions +Wrote PCA transformed file. +Wrote PCA components file. +PCA transformed data. +Will call vbgmm with parameters: outdir/, 400, 1000, 1 +Wrote assign file. +CONCOCT Finished |