--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/comebin.xml	Wed Jul 30 05:56:42 2025 +0000
@@ -0,0 +1,84 @@
+<tool id="comebin" name="COMEBin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Binning of metagenomic contigs using COntrastive Multi-viEw representation learning</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+            
+            #import re
+            
+            mkdir 'outputs' 'bam_files' &&
+
+            #set $safename = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier)
+            ln -s '$assembly_file' '${safename}.fasta' &&
+
+            #for $file in $bam_files:
+                #set $safename = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
+                ln -s '$file' './bam_files/${safename}.bam' &&
+            #end for 
+            
+            run_comebin.sh
+            -a 'assembly_file.fasta'
+            -o 'outputs'
+            -p 'bam_files'
+            -t \${GALAXY_SLOTS:-12}
+            -l ${loss}
+            -n ${learning}
+            -e ${emb_comebin}
+            -c ${emb_cov}
+            -b ${batch}
+        
+        ]]>
+    </command> 
+    <inputs>
+        <param name="assembly_file" type="data" format="fasta" label="Metagenomic assembly file"/>
+        <param name="bam_files" type="data" format="bam" multiple="true" label="Input bam file(s)"/>
+        <param name="learning" type="integer" default_value="6" label="Views for contrastive multiple-view learning"/>
+        <param name="loss" type="float" default_value="0.15" label="Temperature in loss function" help="0.07 is recommended for assemblies with an N50 > 10000"/>
+        <param name="emb_comebin" type="integer" default_value="2048" label="Embedding size for COMEBin network"/>
+        <param name="emb_cov" type="integer" default_value="2048" label="Embedding size for coverage network"/>
+        <param name="batch" type="integer" default_value="1024" label="Batch size"/>
+    </inputs>
+    <outputs>
+        <collection name="bins" type="list" format="fasta" label="${tool.name}: BINS">
+            <discover_datasets pattern="__name__" directory="outputs/comebin_res/comebin_res_bins/"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="assembly_file" ftype="fasta" value="input_single.fasta"/>
+            <param name="bam_files" ftype="bam" value="input_single.bam"/>
+            <param name="learning" value="6"/>
+            <param name="loss" value="0.15"/>
+            <param name="emb_comebin" value="2048"/>
+            <param name="emb_cov" value="2048"/>
+            <param name="batch" value="1024"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+            **IMPORTANT**
+
+            It might happen that this tool will throw out an error. If this error happen: ValueError: max() arg is an empty sequence
+            then try to run this tool with different values it might fix this. When this error happen: UnboundLocalError: local variable 'logits' referenced before assignment
+            then the imputed data might not be enough such that this tool will function correctly.
+
+            Also the run-time of this tool will be high since it is machining learning tool for binning!
+
+            **Input**
+
+            - The assembly file in fasta format
+            - The corresponded bam file(s) to the assembly file
+
+            **Output**
+
+            As output from the tool is a collection of bins created with machining learning
+
+            
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
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