diff cluster_butina_matrix.xml @ 0:0332c2ff19f2 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster_butina_matrix.xml	Tue Jul 21 05:25:09 2020 -0400
@@ -0,0 +1,96 @@
+<tool id="ctb_im_cluster_butina_matrix" name="Butina Cluster Matrix" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>using RDKit</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        cluster_butina_matrix
+            -i '$infile'
+            -if sdf
+            -t '$threshold'
+            -mt '$matrix_threshold'
+            -d '$descriptor_opts'
+            -m '$metric_opts'
+            --meta
+            -o outp
+            -of tsv &>> $logfile &&
+        cat outp_metrics.txt &>> $logfile &&
+        gzip -d outp.tsv.gz
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
+        <param name="threshold" min="0" max="1" type="float" value="0.7" label="Threshold" help="Similarity clustering threshold (1.0 means identical)"/>
+        <param name="matrix_threshold" min="0" max="1" type="float" value="0.5" label="Matrix threshold" help="Threshold for outputting values (1.0 means identical)"/>
+
+        <param name="descriptor_opts" type="select" label="Descriptor Options" help="Descriptor or fingerprint type (default rdkit)">
+            <option value="rdkit" selected="true">rdkit</option>
+            <option value="maccs">maccs</option>
+            <option value="morgan2">morgan2</option>
+            <option value="morgan3">morgan3</option>
+        </param>
+
+        <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient">
+            <option value="tanimoto" selected="true">tanimoto</option>
+            <option value="asymmetric">asymmetric</option>
+            <option value="braunblanquet">braunblanquet</option>
+            <option value="cosine">cosine</option>
+            <option value="dice">dice</option>
+            <option value="kulczynski">kulczynski</option>
+            <option value="mcconnaughey">mcconnaughey</option>
+            <option value="rogotgoldberg">rogotgoldberg</option>
+            <option value="russel">russel</option>
+            <option value="sokal">sokal</option>
+        </param>
+    </inputs>
+
+    <expand macro="outputs" output_format="tsv" filetype="tabular"/>
+
+    <tests>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <param name="descriptor_opts" value="rdkit"/>
+            <param name="metric_opts" value="tanimoto"/>
+            <param name="threshold" value="0.6"/>
+            <param name="matrix_threshold" value="0.5"/>
+            <output name="outfile" ftype="tabular" file="cluster_butina_matrix_output1.tsv"/>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="Found 30 clusters"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool performs Butina clustering for a set of input molecules, using the chemistry toolkit RDKit, and returns results in tabular format.
+
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - Molecules in `SDF format`_
+| - A number of other parameters can be set, including the fingerprint type and the similarity metric to use.
+
+.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
+
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+Tabular file containing clusters.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file