diff recetox_aplcms_compute_clusters.xml @ 0:82737757f3d5 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_compute_clusters.xml	Mon Feb 13 10:27:56 2023 +0000
@@ -0,0 +1,86 @@
+<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy0">
+    <description>compute clusters of mz and rt across samples and assign cluster IDs to individual features</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[
+              #set filenames = str("', '").join([str($f) for $f in $files])
+              feature_tables <- load_parquet_collection(c('$filenames'))
+              sample_names <- unlist(lapply(feature_tables, load_sample_name))
+
+              validate_sample_names(sample_names)
+
+              ordering <- order(sample_names)
+              feature_tables <- feature_tables[ordering]
+              sample_names <- sample_names[ordering]
+
+              #if $tolerances_input_method.input_method == "file"
+              tolerances <- load_data_from_parquet_file('$input_tolerances')
+              #end if
+
+              clusters <- compute_clusters(
+                  feature_tables = feature_tables,
+                  #if $tolerances_input_method.input_method == "file"
+                  mz_tol_relative = get_mz_tol(tolerances),
+                  rt_tol_relative = get_rt_tol(tolerances),
+                  #else
+                  #if $tolerances_input_method.mz_tol_relative:
+                  mz_tol_relative = $tolerances_input_method.mz_tol_relative,
+                  #else:
+                  mz_tol_relative = NA,
+                  #end if
+                  #if $tolerances_input_method.rt_tol_relative:
+                  rt_tol_relative = $tolerances_input_method.rt_tol_relative,
+                  #else:
+                  rt_tol_relative = NA,
+                  #end if
+                  #end if
+                  mz_max_diff = 10 * $mz_max_diff,
+                  mz_tol_absolute = $mz_tol_absolute,
+                  sample_names = sample_names,
+                  do.plot = FALSE
+              )
+
+              save_parquet_collection(clusters, sample_names, "clustered")
+              save_tolerances(clusters, '$tolerances')
+         ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data"
+               help="List of tables containing features." />
+        <expand macro="compute_clusters_params"/>
+    </inputs>
+
+    <outputs>
+        <collection name="clustered_feature_tables" type="list"
+                    label="${tool.name} feature_tables on ${on_string}">
+            <discover_datasets pattern="__designation__" directory="clustered" format="parquet" />
+        </collection>
+        <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (updated tolerances)" />
+    </outputs>
+
+    <tests>
+
+    </tests>
+
+    <help>
+        <![CDATA[
+            @COMPUTE_CLUSTERS_HELP@
+
+            @GENERAL_HELP@
+
+            @EXAMPLE_OUTPUT@
+        ]]>
+    </help>
+
+    <expand macro="citations"/>
+</tool>