Mercurial > repos > recetox > filter_compounds

changeset 1:686850eb1e64 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:21:21 +0000
parents 987357c6941c
children 8eb6e392c92b
files filter_compounds.xml macros.xml
diffstat 2 files changed, 46 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/filter_compounds.xml	Thu Jan 07 11:30:13 2021 +0000
+++ b/filter_compounds.xml	Fri Jan 28 16:21:21 2022 +0000
@@ -5,48 +5,46 @@
         <import>macros.xml</import>
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
+    <expand macro="creator"/>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
-<![CDATA[
-    python '$__tool_directory__/filter_compounds.py'
-      -i '${infile}'
-      -o '${outfile}'
-      $metorg
-      $anorg
-]]>
+        <![CDATA[
+            python '$__tool_directory__/filter_compounds.py'
+              -i '${infile}'
+              -o '${outfile}'
+              $metorg
+              $anorg
+        ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="smi" label="Select input file" help="Currently only SMILES identifiers are allowed as an input."/>
-        <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Filter out organometallic compounds?" />
-        <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Filter out anorganic compounds?" />
+        <param name="infile" type="data" format="smi" label="Select input file"
+               help="Currently only SMILES identifiers are allowed as an input."/>
+        <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue=""
+               label="Filter out organometallic compounds?"/>
+        <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue=""
+               label="Filter out anorganic compounds?"/>
     </inputs>
     <outputs>
-	    <data format="smi" name="outfile"/>
+        <data format="smi" name="outfile"/>
     </outputs>
     <tests>
         <test>
             <param name="infile" ftype="smi" value="input_all.smi"/>
             <param name="metorg" value="true"/>
-            <param name="anorg" value="true"/>	
-            <output name="outfile" ftype="smi" file="output_all.smi" />
+            <param name="anorg" value="true"/>
+            <output name="outfile" ftype="smi" file="output_all.smi"/>
         </test>
         <test>
             <param name="infile" ftype="smi" value="input_all_table.smi"/>
             <param name="metorg" value="true"/>
             <param name="anorg" value="true"/>
-            <output name="outfile" ftype="smi" file="output_all_table.smi" />
+            <output name="outfile" ftype="smi" file="output_all_table.smi"/>
         </test>
     </tests>
     <help>
-<![CDATA[
-
-.. class:: infomark
-
-**What this tool does**
-
-Filters organometallics (compounds containing atoms other than C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K) or anorganics (compounds without C). Input can be either list of SMILES identifiers or indexed table of SMILES (two tab-separated columns, first column is index, second columns is SMILES).
-
-]]>
+        <![CDATA[
+            @HELP@
+        ]]>
     </help>
 </tool>
 
--- a/macros.xml	Thu Jan 07 11:30:13 2021 +0000
+++ b/macros.xml	Fri Jan 28 16:21:21 2022 +0000
@@ -1,6 +1,19 @@
 <macros>
     <token name="@TOOL_VERSION@">3.1.1</token>
 
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Karolína"
+                familyName="Trachtová"
+                url="https://github.com/trachtok" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement>
@@ -14,4 +27,16 @@
             <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
         </stdio>
     </xml>
+
+    <token name="@HELP@">
+        <![CDATA[
+            .. class:: infomark
+
+            **What this tool does**
+
+            Filters organometallics (compounds containing atoms other than C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K) or
+            anorganics (compounds without C). Input can be either list of SMILES identifiers or indexed table of SMILES
+            (two tab-separated columns, first column is index, second columns is SMILES).
+        ]]>
+    </token>
 </macros>