Mercurial > repos > recetox > riassigner

changeset 3:113f5f66e6b9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:30:37 +0000
parents 3c396ae0a1e7
children 97c020d36c8f
files macros.xml riassigner.xml
diffstat 2 files changed, 23 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Jan 25 09:39:36 2022 +0000
+++ b/macros.xml	Fri Jan 28 16:30:37 2022 +0000
@@ -2,14 +2,24 @@
     <token name="@TOOL_VERSION@">0.3.1</token>
     <xml name="creator">
         <creator>
+            <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>
+
     <token name="@HELP@">
         <![CDATA[
-        RIAssigner can be used to read data from .msp, .csv and .tsv files using matchms and pandas and to compute the retention indices for the data. A reference list of retention indexed compounds (traditionally an Alkane series) with retention times is used to compute the RI for a query dataset of retention time values using the van den Dool method or by using cubic spline based interpolation.
+        RIAssigner can be used to read data from .msp, .csv and .tsv files using matchms and pandas and to compute the
+        retention indices for the data. A reference list of retention indexed compounds (traditionally an Alkane series)
+        with retention times is used to compute the RI for a query dataset of retention time values using the van den
+        Dool method or by using cubic spline based interpolation.
         ]]>
     </token>
 </macros>
--- a/riassigner.xml	Tue Jan 25 09:39:36 2022 +0000
+++ b/riassigner.xml	Fri Jan 28 16:30:37 2022 +0000
@@ -3,10 +3,11 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="creator"/>
+
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
     </requirements>
-    <expand macro="creator"/>
 
     <command detect_errors="exit_code"><![CDATA[
         python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${query_section.query.ext}" &&
@@ -37,28 +38,30 @@
                 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
                 ]]></help>
             </param>
-            <param name="reference_rt_units" type="select" display="radio" help="Retention time units in the reference file.">
+            <param name="reference_rt_units" type="select" display="radio"
+                   help="Retention time units in the reference file.">
                 <option value="seconds" selected="true">Seconds</option>
                 <option value="min">Minutes</option>
             </param>
         </section>
         <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
             <option value="kovats" selected="true">Kovats</option>
-            <option value="cubicspline">CubicSpline </option>
+            <option value="cubicspline">CubicSpline</option>
         </param>
     </inputs>
 
     <outputs>
-        <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" metadata_source="query"/>
+        <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query"
+              metadata_source="query"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv" />
-            <param name="query_rt_units" value="seconds" />
-            <param name="reference" value="Alkanes_20210325.csv" ftype="csv" />
-            <param name="reference_rt_units" value="seconds" />
-            <param name="method" value="kovats" />
+            <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/>
+            <param name="query_rt_units" value="seconds"/>
+            <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/>
+            <param name="reference_rt_units" value="seconds"/>
+            <param name="method" value="kovats"/>
             <output name="output" file="results.csv" ftype="csv"/>
         </test>
     </tests>