Mercurial > repos > recetox > gc_derivatization

changeset 0:600b391827e3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization commit b757d35278216a1f43bd53ea687a951b005e47df
author recetox
date Wed, 20 Mar 2024 12:20:23 +0000
parents
children
files gc_derivatization.xml macros.xml test-data/input.tabular
diffstat 3 files changed, 81 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gc_derivatization.xml	Wed Mar 20 12:20:23 2024 +0000
@@ -0,0 +1,56 @@
+<tool id="gc_derivatization" name="GC derivatization" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+    <description>In silico MeOX and TMS derivatization tool</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">gc-meox-tms</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+    python -m gc_meox_tms -t '${output}' '${input}'
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="smi,tabular" help="SMILES list in smi or tabular formats."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.tabular" ftype="smi"/>
+            <output name="output" >
+                <assert_contents>
+                    <has_text text="CC(N)=O"/>
+                    <has_text text="CC(=O)O"/>
+                    <has_text text="CC=NOC"/>
+                    <has_text text="OC1=CC=CC=C1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+        The tool outputs a table with multiple columns containing the original SMILES as well as with the derivatization group removed.
+        The further columns contain all possible derivatized forms of the molecule. See the example output below.
+
+        +----------------+----------------+-------------------------+--------------------+---------------------------------+
+        | orig           | deriv. removed | deriv. added            | ...                |                                 |
+        +================+================+=========================+====================+=================================+
+        | CC(N)=O        | CC(N)=O        | CC(N)=O                 | CC(=O)N[Si](C)(C)C | CC(=O)N([Si](C)(C)C)[Si](C)(C)C |
+        +----------------+----------------+-------------------------+--------------------+---------------------------------+
+        | OC1=CC=CC=C1   | OC1=CC=CC=C1   | C[Si](C)(C)OC1=CC=CC=C1 | OC1=CC=CC=C1       |                                 |
+        +----------------+----------------+-------------------------+--------------------+---------------------------------+
+        | CC(=O)O        | CC(=O)O        | CC(=O)O[Si](C)(C)C      | CC(=O)O            |                                 |
+        +----------------+----------------+-------------------------+--------------------+---------------------------------+
+        | CC=NOC         | CC=O           | CC=NOC                  |                    |                                 |
+        +----------------+----------------+-------------------------+--------------------+---------------------------------+
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">https://doi.org/10.1021/acs.analchem.7b01010</citation>
+    </citations>     
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Mar 20 12:20:23 2024 +0000
@@ -0,0 +1,21 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.1</token>
+    <xml name="creator">
+    <creator>
+        <person
+            givenName="Wudmir"
+            familyName="Rojas"
+            url="https://github.com/wverastegui"
+            identifier="0000-0001-7036-9987" />
+        <person
+            givenName="Helge"
+            familyName="Hecht"
+            url="https://github.com/hechth"
+            identifier="0000-0001-6744-996X" />
+        <organization
+            url="https://www.recetox.muni.cz/"
+            email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+            name="RECETOX MUNI"/>
+    </creator>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.tabular	Wed Mar 20 12:20:23 2024 +0000
@@ -0,0 +1,4 @@
+CC(N)=O
+OC1=CC=CC=C1
+CC(=O)O
+CC=NOC
\ No newline at end of file