# HG changeset patch
# User iuc
# Date 1645193868 0
# Node ID 1bc8fd1b3ed0bda31b69440fd263256e19dc46a7

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"

diff -r 000000000000 -r 1bc8fd1b3ed0 extract_fasta_bins.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_fasta_bins.py	Fri Feb 18 14:17:48 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')
diff -r 000000000000 -r 1bc8fd1b3ed0 extract_fasta_bins.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_fasta_bins.xml	Fri Feb 18 14:17:48 2022 +0000
@@ -0,0 +1,58 @@
+<tool id="concoct_extract_fasta_bins" name="Extract a fasta file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>for each cluster in a CONCOCT clustering file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+mkdir outdir &&
+python '$__tool_directory__/extract_fasta_bins.py'
+#if $input_fasta.is_of_type('fasta.gz'):
+    --gzipped
+#end if
+--input_fasta '$input_fasta'
+--input_cluster '$input_cluster'
+--output_path 'outdir'
+    ]]></command>
+    <inputs>
+        <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="Fasta file"/>
+        <param argument="--input_cluster" type="data" format="tabular" label="CONCOCT clustering file"/>
+    </inputs>
+    <outputs>
+        <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outdir"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="input1.fa.gz" ftype="fasta.gz"/>
+            <param name="input_cluster" value="inputcluster1.tabular" ftype="tabular"/>
+            <output_collection name="bins" type="list" count="2">
+                <element name="77" ftype="fasta">
+                    <assert_contents>
+                        <has_size value="2194"/>
+                        <has_text text="NODE_1_length_2054_cov_17.474684"/>
+                        <has_n_lines n="37"/>
+                    </assert_contents>
+                </element>
+                <element name="93" ftype="fasta">
+                    <assert_contents>
+                        <has_size value="16531"/>
+                        <has_text text="NODE_2_length_16156_cov_8.219856"/>
+                        <has_n_lines n="272"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Performs metagenomic binning of fasta contigs by extracting a fasta file for each cluster defined in a
+CONCOCT clustering file.
+
+The tool accepts two inputs; the fasta contigs file and the CONCOCT clustering file that was produced using
+the same fasta contigs input.  A collection of fasta files is produced.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 1bc8fd1b3ed0 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Feb 18 14:17:48 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>
diff -r 000000000000 -r 1bc8fd1b3ed0 test-data/input1.fa.gz
Binary file test-data/input1.fa.gz has changed
diff -r 000000000000 -r 1bc8fd1b3ed0 test-data/input1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.tabular	Fri Feb 18 14:17:48 2022 +0000
@@ -0,0 +1,417 @@
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+NODE_283_length_165_cov_4.200000	235	0.851064	1.276595	0.851063	0	0	0	0	0	0.425532	2.127663	0.425532	0.425532	0.425532	0	0.425532	2.127663
+NODE_284_length_148_cov_4.236486	218	0.917431	0.454128	0	0.458716	0	0	0	2.752293	0.458716	0.422018	0	2.293577	0	0.917431	3.211007	0.917431
+NODE_285_length_433_cov_5.106236	503	1.590457	2.582506	3.165008	0	0	0	4.165009	0	2.783302	0.994036	0.198807	1.192843	2.972167	3.976146	1.391651	0.984095
+NODE_288_length_174_cov_4.316092	244	2.049180	1.639345	1.229508	0	0	0	2.036885	0	2.036885	0.409836	0.409836	0.409836	2.032786	1.229508	0.409836	3.278688
+NODE_28_length_34835_cov_8.108799.0	10000	1.908700	4.387700	2.947500	0	0	0	3.797100	0	4.693900	0.987500	0.349000	1.328800	4.478800	5.105200	2.888500	1.397900
+NODE_28_length_34835_cov_8.108799.1	10000	1.847500	4.356800	2.648600	0	0	0	3.735900	0	3.876700	1.019300	0.259600	1.159900	3.745800	4.606000	2.606500	1.108800
+NODE_28_length_34835_cov_8.108799.2	14905	1.775715	4.499630	2.730357	0	0	0	3.825425	0	4.424353	0.944917	0.315331	1.307078	3.888697	4.907619	2.850249	1.540825
+NODE_290_length_1962_cov_6.746177	2032	1.525591	5.413389	2.944881	0	0	0	4.079231	0	3.885336	0.929626	0.049213	1.427166	4.221458	4.773624	1.968506	1.377954
+NODE_293_length_832_cov_6.325721	902	3.436805	4.988915	4.101994	0	0	0	4.758316	0	7.283812	1.108646	0.442350	3.092018	5.518847	4.317073	4.529935	1.771619
+NODE_294_length_210_cov_4.066667	280	2.142857	1.414286	0.357143	0	0	0	0.357143	0	0.357143	2.499999	0.357143	0	1.071428	0	1.071428	1.785713
+NODE_295_length_196_cov_4.397959	266	1.879699	0.375940	1.127819	0	0	0	0.751880	0	0.375940	3.349628	0	0	0	0	0.375940	0.751880
+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
diff -r 000000000000 -r 1bc8fd1b3ed0 test-data/inputcluster1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcluster1.tabular	Fri Feb 18 14:17:48 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
diff -r 000000000000 -r 1bc8fd1b3ed0 test-data/process_log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/process_log.txt	Fri Feb 18 14:17:48 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