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changeset 0:06c0eb033025 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
author iuc
date Fri, 18 Feb 2022 14:18:11 +0000
parents
children 031f84cb2fd3
files 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
diffstat 7 files changed, 612 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concoct.xml	Fri Feb 18 14:18:11 2022 +0000
@@ -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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_fasta_bins.py	Fri Feb 18 14:18:11 2022 +0000
@@ -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')
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Feb 18 14:18:11 2022 +0000
@@ -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>
Binary file test-data/input1.fa.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.tabular	Fri Feb 18 14:18:11 2022 +0000
@@ -0,0 +1,417 @@
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+NODE_29_length_44540_cov_9.429951.0	10000	2.027900	5.076300	3.653900	0	0	0	4.475300	0	4.737900	2.168800	0.700000	1.458700	4.274900	4.467800	3.147200	3.525100
+NODE_29_length_44540_cov_9.429951.1	10000	2.258300	4.988600	3.198400	0	0	0	3.565800	0	4.268500	2.740000	0.570000	1.366900	4.895400	4.835200	3.426900	4.108300
+NODE_29_length_44540_cov_9.429951.2	10000	2.716900	5.218600	3.607200	0	0	0	3.996700	0	4.797500	3.179400	0.770000	1.508700	4.924600	4.254900	3.564600	4.146500
+NODE_29_length_44540_cov_9.429951.3	14610	2.230117	5.066739	3.647501	0	0	0	4.351748	0	4.827725	1.531828	0.342231	1.298221	4.664888	5.032990	3.008352	2.216154
+NODE_2_length_16156_cov_8.219856	16226	1.545114	4.323432	2.912856	0	0	0	3.922715	0	4.290770	0.992173	0.388265	1.182792	4.050168	5.099648	2.813631	1.411069
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcluster1.tabular	Fri Feb 18 14:18:11 2022 +0000
@@ -0,0 +1,3 @@
+contig_id	cluster_id
+NODE_1_length_2054_cov_17.474684	77
+NODE_2_length_16156_cov_8.219856	93
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/process_log.txt	Fri Feb 18 14:18:11 2022 +0000
@@ -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