diff recetox_aplcms_correct_time.xml @ 0:4d7db9cdd952 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_aplcms_correct_time.xml	Mon Feb 13 10:28:51 2023 +0000
@@ -0,0 +1,65 @@
+<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0">
+    <description>correct retention time across samples for peak alignment</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>help.xml</import>
+    </macros>
+    <expand macro="creator"/>
+    <expand macro="requirements"/>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
+    ]]></command>
+    <configfiles>
+         <configfile name="run_script"><![CDATA[
+              features_table <- load_data_from_parquet_file('$features_table')
+              sample_name <- load_sample_name(features_table)
+
+              if(is.na(sample_name)) {
+                  message("The file does not contain sample name.")
+              }
+
+              template_features <- load_data_from_parquet_file('$template')
+              tolerances <- load_data_from_parquet_file('$tolerances')
+
+              corrected_table <- correct_time(
+                   this.feature = features_table,
+                   template_features = template_features,
+                   mz_tol_relative = get_mz_tol(tolerances),
+                   rt_tol_relative = get_rt_tol(tolerances)
+              )
+
+              corrected_table <- save_sample_name(corrected_table, sample_name)
+              save_data_as_parquet_file(corrected_table, '$output_file')
+         ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param label="Input clustered features table" name="features_table" type="data" format="parquet"
+               help="Mass spectrometry clustered features table." />
+        <param label="Input template features table" name="template" type="data" format="parquet"
+               help="Template features table." />
+        <param label="Input tolerances values" name="tolerances" type="data" format="parquet"
+               help="Table containing tolerance values." />
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
+    </outputs>
+
+    <tests>
+
+    </tests>
+
+    <help>
+        <![CDATA[
+            @CORRECT_TIME_HELP@
+
+            @GENERAL_HELP@
+
+            @EXAMPLE_OUTPUT@
+        ]]>
+    </help>
+
+    <expand macro="citations"/>
+</tool>