update fragmentation wrappers to the 0.2 version

Author: bgruening

biopython/tools/base_distribution.py biopython/base_distribution.py

@@ -8,7 +8,6 @@
         --output-format $oformat 
         -r $rules 
         $mark
-
     2>&1
   </command>
   <inputs>

biopython/tools/base_distribution.xml biopython/base_distribution.xml

@@ -1,16 +1,34 @@
 <tool id="bgchem_fragment_merger" name="Merging" >
   <description>fragmented molecules</description>
   <command interpreter='python' >
-    merger.py -i $infile --input-format ${infile.ext} -o $outfile --output-format $oformat 2>&#38;1
+    merger.py 
+        -i $infile 
+        -o $outfile 
+        --molwt-cutoff $molwt_cutoff 
+        #if $iter_opts.iter_opts_selector=="user":
+            --mdid-off # if set, its deactivated
+            --max-iteration-depth $iter_opts.max_depth
+        #else:
+            ## Set defaults
+        ## End of molecule dependent iteration depth options:
+        #end if
+        2>&#38;1
   </command>
   <inputs>
     <param name="infile" type="data" format="sdf,smi,mol,inchi,cml" label="Input file" help="Dataset missing? See TIP below"/>
-    <param name='oformat' type='select' format='text' label="Output format.">
-        <option value='smi'>SMILES</option>
-        <option value='inchi'>InChI</option>
-        <option value='sdf'>SD-Files</option>
-        <option value='mol2'>mol2</option>
-    </param>
+    <param name="molwt_cutoff" type="integer" value="500" label="The number of positions between windows to report."/>
+    <conditional name="iter_opts">
+        <param name="iter_opts_selector" type="select" label="Iteration depth">
+            <option value="mdid" selected="True">Molecule dependent iteration depth</option>
+            <option value="user">User dependent iteration depth</option>
+        </param>
+        <when value="mdid" />
+        <when value="user">
+            <param name="max_depth" type="integer" value="2" label="Max iteration depth." help="">
+                <validator type="in_range" min="0" />
+            </param>
+        </when>
+    </conditional>
   </inputs>
   <outputs>
    <data format="smi" name="outfile">
@@ -25,7 +43,6 @@
     <test>
     </test>
  </tests>
-
 <help>
 
 
@@ -34,32 +51,13 @@ Merging small molecules together to larger compounds using some predifined react
 
 -----
 
-**Example**
+**Input**
 
-* input:: Fragments
+A molecule file with marked molecules. You can create such a file with the Fragmenter tool and the option 'mark atoms'.
 
+**Output**
 
-** Reaction Matrix **
-0,1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
-1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0
-0,1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
-1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
-1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0
-0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1
-0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0
+A molecule file with new created/merged molecules.
 
 
  </help>