--- /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>