diff sygma.xml @ 1:0e330829de40 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sygma commit 5b2d7437ba0875c0913630fd2165c82ed933422c"

--- a/sygma.xml	Mon Sep 30 17:38:26 2019 -0400
+++ b/sygma.xml	Sun Mar 15 13:18:38 2020 -0400
@@ -1,27 +1,31 @@
-<tool id="sygma" name="Generate possible metabolites with SyGMa" version="@VERSION@">
+<tool id="sygma" name="Generate possible metabolites with SyGMa" version="@VERSION@+galaxy1">
+    <description>by performing common reactions on one or more parent molecule(s)</description>
     <macros>
         <token name="@VERSION@">1.1.1</token>
     </macros>
-    <description>by performing common reactions on one or more parent molecule(s)</description>
     <requirements>
         <requirement type="package" version="@VERSION@">sygma</requirement>
         <requirement type="package" version="2019.03.4">rdkit</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/sygma_metabolites.py' 
-            -i '$input' 
-            --iformat '$input.ext' 
-            -o '$output' 
-            --phase1 '$phase1' 
+        python '$__tool_directory__/sygma_metabolites.py'
+            -i '$input'
+            --iformat '$input.ext'
+            -o '$output'
+            --phase1 '$phase1'
             --phase2 '$phase2'
+            #if $detailed
+              --detailed
+            #end if
     ]]></command>
     <inputs>
         <param type="data" name="input" format="smi,sdf" label="Parent molecule(s)" help="Upload an SDF or SMILES file."/>
         <param type="integer" name="phase1" value="1" min="0" label="Number of reaction cycles to apply for phase 1" help="Phase 1 metabolism rules include different types of oxidation, reduction, hydrolysis and condensation reactions."/>
         <param type="integer" name="phase2" value="1" min="0" label="Number of reaction cycles to apply for phase 2" help="Phase 2 metabolism rules include several conjugation reactions, e.g. with glucuronyl, sulfate, methyl or acetyl."/>
+        <param type="boolean" name="detailed" label="Include more detailed information" help="Will return detailed information including molecular formula of the chemical structure and transformation pathway involved."/>
     </inputs>
     <outputs>
-        <data name="output" format="smi"/>
+        <data name="output" format="tsv"/>
     </outputs>
     <tests>
         <test>
@@ -31,6 +35,13 @@
             <output name="output" file="o.smi"/>
         </test>
         <test>
+            <param name="input" value="i.smi" ftype="smi"/>
+            <param name="phase1" value="1"/>
+            <param name="phase2" value="1"/>
+            <param name="detailed" value="true"/>
+            <output name="output" file="o_detailed.smi"/>
+        </test>
+        <test>
             <param name="input" value="i.sdf" ftype="sdf"/>
             <param name="phase1" value="2"/>
             <param name="phase2" value="0"/>
@@ -44,8 +55,8 @@
 
 **What this tool does**
 
-SyGMa (Systematic Generation of potential Metabolites) is a tool to generate 
-possible metabolic products of an input parent structure. The tool provides 
+SyGMa (Systematic Generation of potential Metabolites) is a tool to generate
+possible metabolic products of an input parent structure. The tool provides
 two rulesets to cover both phase 1 and 2 metabolism.
 
 -----
@@ -54,11 +65,11 @@
 
 **Input**
 
-A file in SMILES or SDF format. Files may contain multiple molecule 
-entries; in this case outputs are distinguished by the code included in the 
+A file in SMILES or SDF format. Files may contain multiple molecule
+entries; in this case outputs are distinguished by the code included in the
 output file (e.g. SYGMA0MOL0 vs SYGMA1MOL0).
 
-The number of reaction cycles to be performed for both phase 1 and phase 2 
+The number of reaction cycles to be performed for both phase 1 and phase 2
 metabolism should also be specified.
 
 -----
@@ -67,25 +78,32 @@
 
  **Output**
 
-For each molecule in the input file, a SMILES file is produced containing 
-SMILES strings of the metabolite outputs, a generated ID code, and an empirical 
-probability score (corresponding to an estimated probability that a product is 
+A tab-separated values (tsv) file for each molecule in the input file.
+Columns contain a generated ID code (compound_id), SMILES strings of the
+metabolite outputs (smiles) and an empirical probability score (sygma_score).
+Calculated score value corresponds to an estimated probability that a product is
 actually metabolically produced in humans). The first line is always the parent
-molecule itself::
+molecule itself.
 
-    Oc1ccccc1   SYGMA0MOL0    1.0
-    O=C(O)C1OC(Oc2ccccc2)C(O)C(O)C1O    SYGMA0MOL1 0.25
-    O=S(=O)(O)Oc1ccccc1 SYGMA0MOL2  0.119
-    Oc1ccc(O)cc1    SYGMA0MOL3 0.056
-    COc1ccccc1  SYGMA0MOL4   0.054
-    Oc1ccccc1O  SYGMA0MOL5   0.032
-    O=C(O)C1OC(Oc2ccc(O)cc2)C(O)C(O)C1O SYGMA0MOL6  0.014
-    O=C(O)C1OC(Oc2ccccc2O)C(O)C(O)C1O   SYGMA0MOL7    0.008
-    O=S(=O)(O)Oc1ccc(O)cc1  SYGMA0MOL8   0.00666
-    O=S(=O)(O)Oc1ccccc1O    SYGMA0MOL9 0.00381
-    COc1ccc(O)cc1   SYGMA0MOL10   0.00302
-    COc1ccccc1O SYGMA0MOL11 0.00173
++----------------------------------+-------------+-------------+
+| smiles                           | compound_id | sygma_score |
++----------------------------------+-------------+-------------+
+| Oc1ccccc1                        | SYGMA0MOL0  | 1.0         |
++----------------------------------+-------------+-------------+
+| O=C(O)C1OC(Oc2ccccc2)C(O)C(O)C1O | SYGMA0MOL1  | 0.25        |
++----------------------------------+-------------+-------------+
 
+If option for more detailed output is selected, additional columns include
+molecular formula (molecular_formula) of the chemical structure, number of
+reactions (sygma_n) and transformation pathway (sygma_pathway) involved.
+
++----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
+| smiles                           | compound_id | sygma_score  | molecular_formula | sygma_n  | sygma_pathway                         |
++----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
+| Oc1ccccc1                        | SYGMA0MOL0  | 1.0          | C6H6O             | 1        | parent                                |
++----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
+| O=C(O)C1OC(Oc2ccccc2)C(O)C(O)C1O | SYGMA0MOL1  | 0.25         | C12H14O7          | 2        | O-glucuronidation_(aromatic_hydroxyl) |
++----------------------------------+-------------+--------------+-------------------+----------+---------------------------------------+
 
     ]]></help>
     <citations>