--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin.xml	Fri Oct 14 21:48:47 2022 +0000
@@ -0,0 +1,165 @@
+<tool id="semibin_bin" name="SemiBin: Group the contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        into bins
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+@FASTA_FILES@
+SemiBin bin
+    --input-fasta 'contigs.fasta'
+    --data '$data'
+#if $mod.select == 'history'
+    --model '$mod.model'
+#else
+    --environment '$mod.environment'
+#end if
+    --output 'output'
+    --threads \${GALAXY_SLOTS:-1}
+    --minfasta-kbs $minfasta_kbs
+    $no_recluster
+    --max-node $max_node
+    --max-edges $max_edges
+    --random-seed $random_seed
+    @MIN_LEN@
+    --orf-finder '$orf_finder'
+    ]]></command>
+    <inputs>
+        <expand macro="mode_fasta"/>
+        <expand macro="data"/>
+        <conditional name="mod">
+            <param name="select" type="select" label="Model to use">
+                <option value="built-in" selected="true">Built-in model</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="built-in">
+                <expand macro="environment"/>
+            </when>
+            <when value="history">
+                <param argument="--model" type="data" format="h5" label="Trained semi-supervised deep learning model"/>
+            </when>
+        </conditional>
+        <expand macro="min_len"/>
+        <expand macro="orf-finder"/>
+        <expand macro="random-seed"/>
+        <expand macro="max-node"/>
+        <expand macro="max-edges"/>
+        <expand macro="minfasta-kbs"/>
+        <expand macro="no-recluster"/>
+    </inputs>
+    <outputs>
+        <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
+            <filter>not no_recluster</filter>
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
+        </collection>
+        <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+            </conditional>
+            <param name="data" ftype="csv" value="data.csv"/>
+            <conditional name="mod">
+                <param name="select" value="history"/>
+                <param name="model" ftype="h5" value="model.h5"/>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="0" />
+            </conditional>
+            <param name="orf_finder" value="prodigal"/>
+            <param name="random-seed" value="0"/>
+            <param name="max_node" value="1"/>
+            <param name="max_edges" value="200"/>
+            <param name="minfasta_kbs" value="200"/>
+            <param name="no_recluster" value="false"/>
+            <output_collection name="output_recluster_bins" count="0"/>
+            <output_collection name="output_bins" count="3">
+                <element name="0" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g1k_0"/>
+                        <has_text text=">g4k_9"/>
+                    </assert_contents>
+                </element>
+                <element name="1" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g2k_0"/>
+                        <has_text text=">g2k_9"/>
+                    </assert_contents>
+                </element>
+                <element name="2" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g3k_0"/>
+                        <has_text text=">g3k_9"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+            </conditional>
+            <param name="data" ftype="csv" value="data.csv"/>
+            <conditional name="mod">
+                <param name="select" value="built-in"/>
+                <param name="environment" value="human_gut"/>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="0" />
+            </conditional>
+            <param name="orf_finder" value="prodigal"/>
+            <param name="random-seed" value="0"/>
+            <param name="max_node" value="1"/>
+            <param name="max_edges" value="200"/>
+            <param name="minfasta_kbs" value="200"/>
+            <param name="no_recluster" value="true"/>
+            <output_collection name="output_bins" count="3">
+                <element name="0" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g1k_0"/>
+                        <has_text text=">g4k_9"/>
+                    </assert_contents>
+                </element>
+                <element name="1" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g2k_0"/>
+                        <has_text text=">g2k_9"/>
+                    </assert_contents>
+                </element>
+                <element name="2" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g3k_0"/>
+                        <has_text text=">g3k_9"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Inputs
+======
+
+@HELP_INPUT_FASTA@
+@HELP_INPUT_BAM@
+
+Outputs
+=======
+
+@HELP_BINS@
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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