Mercurial > repos > bgruening > openbabel_change_title

changeset 7:9c15e92bed39 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:34:42 -0400
parents 3bf4dcc945f9
children a84187d7bda6
files change_title_to_metadata_value.xml macros.xml test-data/2_mol.dat test-data/CO.smarts
diffstat 4 files changed, 11 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/change_title_to_metadata_value.xml	Mon Sep 03 16:40:25 2018 -0400
+++ b/change_title_to_metadata_value.xml	Tue May 07 13:34:42 2019 -0400
@@ -1,5 +1,5 @@
-<tool id="openbabel_change_title" name="Change Title" version="@VERSION@.0">
-    <description>to meta-data value.</description>
+<tool id="openbabel_change_title" name="Change title" version="@VERSION@.0">
+    <description>to metadata value.</description>
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
@@ -14,8 +14,8 @@
 ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/>
-        <param name="key" type="text" format="text" label="Compound Identifier encoded in the SDF file." help="Specify the key name of the SDF metadata, that contains the molecule identifier."/>
+        <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/>
+        <param name="key" type="text" format="text" label="Compound identifier encoded in the SD-file." help="Specify the key name of the SDF metadata which contains the molecule identifier (e.g. 'PUBCHEM_SHAPE_VOLUME')"/>
     </inputs>
     <outputs>
         <expand macro="output_like_input"/>
@@ -34,7 +34,7 @@
 
 **What this tool does**
 
-Changes the title of a molecule file to a metadata value of a given ID in the same molecule file.
+Reassigns the title of a molecule file (SDF or MOL2) to a metadata value of a given ID in the same molecule file. For example, if the metadata identifier chosen is PUBCHEM_SHAPE_VOLUME, then the title of the file (in the first line) will be replaced by the variable listed under PUBCHEM_SHAPE_VOLUME.
 
 -----
 
@@ -52,7 +52,7 @@
 
 **Output**
 
-Same as input with changed title tag.
+Same as input, with changed title tag.
 
 
 ]]>
--- a/macros.xml	Mon Sep 03 16:40:25 2018 -0400
+++ b/macros.xml	Tue May 07 13:34:42 2019 -0400
@@ -1,9 +1,10 @@
 <macros>
-    <token name="@VERSION@">2.4.1</token>
+    <token name="@VERSION@">2.4.2</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.4.1">openbabel</requirement>
+            <requirement type="package" version="3">python</requirement>
             <yield />
         </requirements>
     </xml>
@@ -37,6 +38,3 @@
         </citations>
     </xml>
 </macros>
-
-
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_mol.dat	Tue May 07 13:34:42 2019 -0400
@@ -0,0 +1,2 @@
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CO.smarts	Tue May 07 13:34:42 2019 -0400
@@ -0,0 +1,1 @@
+CO