diff conformers.xml @ 0:b6cdd73f0c14 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/conformers.xml	Tue Jul 21 05:25:54 2020 -0400
@@ -0,0 +1,105 @@
+<tool id="ctb_im_conformers" name="Generate conformers" 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[
+        conformers
+            -i '$infile'
+            -if sdf
+            -n '$num'
+            -a '$attempts'
+            -r '$rmsd'
+            #if $conditional_cluster.cluster_method_opts != 'none'
+                -c '$conditional_cluster.cluster_method_opts'
+                -t '$conditional_cluster.threshold'
+            #end if
+            -e '$emin'
+            -if sdf
+            --meta
+            -of sdf
+            -o outp &>> $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 format"/>
+        <param name="num" type="integer" label="Number of conformers to generate" value="1"/>
+        <param name="rmsd" type="float" value="1.0" min="0" label="RMSD threshold" help="If a conformer is too similar to those already generated (below the RMSD threshold), it is discarded and regenerated."/>
+        <param name="attempts" type="integer" value="0" min="0" label="Number of attempts" help="Conformers which are below the RMSD threshold are regenerated. This parameter controls how many times this regeneration should be attempted before giving up. "/>
+        <conditional name="conditional_cluster">
+            <param name="cluster_method_opts" type="select" label="Cluster method" help="RMSD, TFD (torsion fingerprint deviation) or no clustering.">
+                <option value="none" selected="true">None</option>
+                <option value="rmsd">RMSD</option>
+                <option value="tfd">TFD</option>
+            </param>
+            <when value="rmsd">
+                <param name="threshold" type="float" label="Cluster threshold" value="2.0" min="0" help="Default of 2.0 for RMSD"/>
+            </when>
+            <when value="tfd">
+                <param name="threshold" type="float" label="Cluster threshold" value="0.3" min="0" help="Default of 0.3 for TFD"/>
+            </when>
+            <when value="none">
+            </when>
+        </conditional>
+        <param name="emin" type="integer" value="0" min="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/>
+    </inputs>
+    
+    <expand macro="outputs" />
+    
+    <tests>
+        <test>
+            <param name="infile" ftype='sdf' value="Kinase_inhibs.sdf"/>
+            <param name="num" value="2"/>
+            <param name="cluster_method_opts" value="rmsd"/>
+            <output name="outfile" ftype="sdf">
+            <!-- contents may vary -->
+                <assert_contents>
+                    <has_text text="ConformerNum"/>
+                    <has_size value="207000" delta="10000"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){65,72}?$"/>
+                </assert_contents>
+            </output>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="__InputCount__"/>
+                    <has_text text="__OutputCount__"/>
+                    <has_n_lines n="40" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool generates conformers for a set of input molecules, using the chemistry toolkit RDKit.
+
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - Molecules in `SDF format`_
+| - A number of other parameters can be set; the most important include the number of conformers to generate and the minimum RMSD difference between them.
+
+.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
+
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file containing generated conformers.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>