--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/max_min_picker.xml	Tue Jul 21 05:23:34 2020 -0400
@@ -0,0 +1,98 @@
+<tool id="ctb_im_max_min_picker" name="Pick" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>diverse compounds from a library with Butina clustering</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        max_min_picker
+            -i '$infile'
+            -if sdf
+            -t '$threshold'
+            -d '$descriptor_opts'
+            #if $number != ''
+                -n $number
+            #end if
+            --fragment-method '$fragment_opts'
+            #if $seedfile
+                -s '$seedfile'
+            #end if
+            $out_fragment
+            --meta
+            -o outp
+            -of sdf &>> $logfile &&
+        cat outp_metrics.txt &>> $logfile &&
+        gzip -d outp.sdf.gz
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format"/>     
+        <param name="threshold" type="float" label="Similarity threshold" value="0.7" min="0" max="1" help="1.0 means identical"/>
+        <param name="descriptor_opts" type="select" label="Type of descriptor or fingerprint" help="Default is morgan2">
+            <option value="maccs">maccs</option>
+            <option value="morgan2" selected="true">morgan2</option>
+            <option value="morgan3">morgan3</option>
+        </param>
+        <param name="number" type="integer" optional="true" label="Maximum number to pick for diverse subset selection" help="ABC"/>
+        <param name="fragment_opts" type="select" label="Fragment" help="Approach to find biggest fragment, if more than one is found">
+            <option value="hac" selected="true">Biggest by heavy atom count</option>
+            <option value="mw">Biggest by molecular weight</option>
+        </param>
+        <param name="seedfile" type="data" format="sdf" optional="true" label="Seed file" help="Optional file containing any seed molecules that have already been picked"/>       
+        <param name="out_fragment" type="boolean" label="Output fragment" truevalue="--output-fragment" falsevalue="" help="Output the biggest fragment rather than the original molecule"/>
+    </inputs>    
+    
+    <expand macro="outputs" />
+    
+    <tests>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <param name="threshold" value="0.5"/>
+            <param name="descriptor_opts" value="morgan2" />
+            <param name="fragment_opts" value="hac" />
+            <output name="outfile" ftype='sdf'>
+                <assert_contents>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){33}?$"/>
+                </assert_contents>
+            </output>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="36 candidates 36 total"/>
+                    <has_text text="Output 33 molecules"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This molecule selects a subset from a library, ensuring the subset reflects the diversity of the library overall by applying Butina clustering.
+
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - Compounds in `SDF Format`_
+| - Various options: similarity threshold, type of fingerprint, seem molecule.
+
+.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
+
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file containing picked compounds.
+
+]]></help>
+    <expand macro="citations" />
+</tool>
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