diff recetox_aplcms_generate_feature_table.xml @ 0:2810c956ec39 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_generate_feature_table.xml	Mon Feb 13 10:26:41 2023 +0000
@@ -0,0 +1,78 @@
+<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0">
+    <description>generate feature table from noise-removed HRMS profile data</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[
+             profile <- load_data_from_parquet_file('$profile')
+             sample_name <- load_sample_name(profile)
+
+             if(is.na(sample_name)) {
+                 message("The file does not contain sample name.")
+             }
+
+             feature_table <- prof.to.features(
+                 profile = profile,
+                 bandwidth = $bandwidth,
+                 #if $min_bandwidth:
+                 min_bandwidth = $min_bandwidth,
+                 #else:
+                 min_bandwidth = NA,
+                 #end if
+                 #if $max_bandwidth:
+                 max_bandwidth = $max_bandwidth,
+                 #else:
+                 max_bandwidth = NA,
+                 #end if
+                 sd_cut = c($sd_cut_min, $sd_cut_max),
+                 #if $shape.shape_model == "bi-Gaussian":
+                 sigma_ratio_lim = c($shape.sigma_ratio_lim_min, $shape.sigma_ratio_lim_max),
+                 #else:
+                 sigma_ratio_lim = NA,
+                 #end if
+                 shape_model = "$shape.shape_model",
+                 peak_estim_method = "$peak_estim_method",
+                 component_eliminate = $component_eliminate,
+                 moment_power = $moment_power,
+                 BIC_factor = $BIC_factor,
+                 do.plot = FALSE
+             )
+
+             feature_table <- save_sample_name(feature_table, sample_name)
+             save_data_as_parquet_file(feature_table, '$output_file')
+         ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param label="Input profile data" name="profile" type="data" format="parquet"
+               help="Mass spectrometry profile data." />
+        <expand macro="bandwidth_params"/>
+        <expand macro="generate_feature_table_params"/>
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
+    </outputs>
+
+    <tests>
+
+    </tests>
+
+    <help>
+        <![CDATA[
+            @GENERATE_FEATURE_TABLE_HELP@
+
+            @GENERAL_HELP@
+        ]]>
+    </help>
+
+    <expand macro="citations"/>
+</tool>