# HG changeset patch
# User recetox
# Date 1611681071 0
# Node ID 87f5cf0baf346b120c8d9f8d305cbc91e2c85660
# Parent  d3d9ba599d51945f9d511473c8134302a51d9448
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"

diff -r d3d9ba599d51 -r 87f5cf0baf34 aplcms_hybrid.xml
--- a/aplcms_hybrid.xml	Sun Oct 18 10:36:05 2020 +0000
+++ b/aplcms_hybrid.xml	Tue Jan 26 17:11:11 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy1">
+<tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy2">
     <macros>
         <import>aplcms_macros.xml</import>
     </macros>
@@ -6,12 +6,12 @@
     <expand macro="requirements" />
 
     <command detect_errors="aggressive"><![CDATA[
-        #set file_str = str('", "').join([str($f) for $f in $files])
+        #set file_str = str("', '").join([str($f) for $f in $files])
 
         Rscript
-            -e 'x <- apLCMS::hybrid(
-                    files = c("$file_str"),
-                    known_table = apLCMS::load_known_table_from_hdf("$known_table"),
+            -e "x <- apLCMS::hybrid(
+                    files = c('$file_str'),
+                    known_table = apLCMS::load_known_table_from_hdf('$known_table'),
                     min_exp = $noise_filtering.min_exp,
                     min_pres = $noise_filtering.min_pres,
                     min_run = $noise_filtering.min_run,
@@ -19,9 +19,9 @@
                     baseline_correct = $noise_filtering.baseline_correct,
                     baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
                     intensity_weighted = $noise_filtering.intensity_weighted,
-                    shape_model = "$feature_detection.shape_model",
+                    shape_model = '$feature_detection.shape_model',
                     BIC_factor = $feature_detection.BIC_factor,
-                    peak_estim_method = "$feature_detection.peak_estim_method",
+                    peak_estim_method = '$feature_detection.peak_estim_method',
                     min_bandwidth = $feature_detection.min_bandwidth,
                     max_bandwidth = $feature_detection.max_bandwidth,
                     sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
@@ -36,10 +36,11 @@
                     recover_mz_range = $weak_signal_recovery.recover_mz_range,
                     recover_chr_range = $weak_signal_recovery.recover_chr_range,
                     use_observed_range = $weak_signal_recovery.use_observed_range,
-                    recover_min_count = $weak_signal_recovery.recover_min_count
-                )'
-            -e 'apLCMS::save_peaks_to_hdf("$peaks", x)'
-            -e 'apLCMS::save_known_table_to_hdf("$updated_known_table", x\$updated_known_table)'
+                    recover_min_count = $weak_signal_recovery.recover_min_count,
+                    cluster = as.integer(\${GALAXY_SLOTS:-1})
+                )"
+            -e "apLCMS::save_peaks_to_hdf('$peaks', x)"
+            -e "apLCMS::save_known_table_to_hdf('$updated_known_table', x\\$updated_known_table)" ## NOTE the double \\ because we want cheetah and bash to ignore the $ character
     ]]></command>
 
     <expand macro="inputs">
diff -r d3d9ba599d51 -r 87f5cf0baf34 aplcms_macros.xml
--- a/aplcms_macros.xml	Sun Oct 18 10:36:05 2020 +0000
+++ b/aplcms_macros.xml	Tue Jan 26 17:11:11 2021 +0000
@@ -3,7 +3,7 @@
 
     <xml name="requirements">
         <requirements>
-            <container type="docker">recetox/aplcms:6.6.6-recetox1</container>
+            <container type="docker">recetox/aplcms:6.6.6-recetox2</container>
         </requirements>
     </xml>