diff nxn_clustering.xml @ 7:0d88631bb7de draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e

--- a/nxn_clustering.xml	Fri Mar 23 03:26:33 2018 -0400
+++ b/nxn_clustering.xml	Tue May 07 13:32:50 2019 -0400
@@ -1,10 +1,9 @@
-<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.4">
+<tool id="ctb_chemfp_nxn_clustering" name="NxN clustering" version="1.5">
     <description>of molecular fingerprints</description>
     <requirements>
-        <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2">python</requirement>
-        <requirement type="package" version="2.0.2">matplotlib</requirement>
-        <requirement type="package" version="0.19.0">scipy</requirement>
+        <requirement type="package" version="1.5">chemfp</requirement>
+        <requirement type="package" version="2.2.3">matplotlib</requirement>
+        <requirement type="package" version="1.2.1">scipy</requirement>
         <requirement type="package" version="2.4.1">openbabel</requirement>
     </requirements>
     <command detect_errors="exit_code">
@@ -16,43 +15,44 @@
                 --cluster '$image'
             #end if
             #if str($output_files) in ['both', 'matrix']:
-                --smatrix '$smilarity_matrix'
+                --smatrix '$similarity_matrix'
             #end if
             --oformat '$oformat'
 ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
-        <param name='threshold' type='float' value='0.0' />
+        <param name="infile" type="data" format="fps" label="Fingerprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' label='Threshold' type='float' value='0.0' />
         <param name='oformat' type='select' format='text' label="Format of the resulting picture">
             <option value='png'>PNG</option>
             <option value='svg'>SVG</option>
         </param>
         <param name='output_files' type='select' format='text' label="Output options">
-            <option value='both'>NxN matrix and Image</option>
+            <option value='both'>NxN matrix and image</option>
             <option value='image'>Image</option>
-            <option value='matrix'>NxN Matrix</option>
+            <option value='matrix'>NxN ḿatrix</option>
         </param>
 
     </inputs>
     <outputs>
-        <data name="image" format="svg" label="${tool.name} on ${on_string} - Cluster Image">
+        <data name="image" format="svg" label="${tool.name} on ${on_string} - Dendrogram Image">
             <filter>output_files == "both" or output_files == "image"</filter>
             <change_format>
                 <when input="oformat" value="png" format="png"/>
             </change_format>
         </data>
-        <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix">
+        <data name="similarity_matrix" format="txt" label="${tool.name} on ${on_string} - Similarity Matrix">
             <filter>output_files == "both" or output_files == "matrix"</filter>
         </data>
     </outputs>
     <tests>
         <test>
             <param name="infile" ftype="fps" value="targets.fps" />
-            <param name='treshold' value='0.75' />
+            <param name='threshold' value='0.75' />
             <param name='oformat' value='svg' />
-            <param name='output_files' value='image' />
-            <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg" compare="sim_size"/>
+            <param name='output_files' value='both' />
+            <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg"/>
+            <output name="similarity_matrix" file='NxN_Clustering_on_q.txt' ftype="txt"/>
         </test>
     </tests>
     <help>
@@ -62,8 +62,7 @@
 
 **What this tool does**
 
-Generating hierarchical clusters and visualizing clusters with dendrograms.
-For the clustering and the fingerprint handling the chemfp_ project is used.
+Based on a set of fingerprints, generates a square self-similarity (NxN) matrix, as well as a dendrogram visualizing the clusters derived from it using hierarchical clustering. For the clustering and the fingerprint handling the chemfp_ project is used.
 
 .. _chemfp: http://chemfp.com/
 
@@ -73,7 +72,7 @@
 
 **Hint**
 
-The plotting of the cluster image is sensible only with a small dataset.
+The plotting of the dendrogram is sensible only with a small dataset - if more than around 20 fingerprints are used the plot will be unreadable.
 
 -----