diff recetox_aplcms_hybrid.xml @ 0:1633a2a34255 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_aplcms_hybrid.xml	Tue Mar 22 16:10:17 2022 +0000
@@ -0,0 +1,100 @@
+<tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy3">
+    <description>generate a feature table from LC/MS spectra</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        sh ${symlink_inputs} &&
+        Rscript  -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
+    ]]></command>
+    <configfiles>
+        <configfile name="symlink_inputs">
+            #for $infile in $files
+                ln -s '${infile}' '${infile.element_identifier}'
+            #end for
+        </configfile>
+        <configfile name="run_script"><![CDATA[
+            #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
+
+            hybrid_main(
+                sample_files = c('$filenames_str'),
+                known_table_file = '${known_table}',
+                updated_known_table_file = '${updated_known_table}',
+                pairing_file = '${feature_known_table_pairing}',
+                aligned_file = '${aligned_feature_sample_table}',
+                recovered_file = '${recovered_feature_sample_table}',
+                out_format = '$output_format.out_format',
+                min_exp = $noise_filtering.min_exp,
+                min_pres = $noise_filtering.min_pres,
+                min_run = $noise_filtering.min_run,
+                mz_tol = $noise_filtering.mz_tol,
+                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',
+                BIC_factor = $feature_detection.BIC_factor,
+                peak_estim_method = '$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, $feature_detection.sd_cut_max),
+                sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
+                component_eliminate = $feature_detection.component_eliminate,
+                moment_power = $feature_detection.moment_power,
+                align_chr_tol = $peak_alignment.align_chr_tol,
+                align_mz_tol = $peak_alignment.align_mz_tol,
+                max_align_mz_diff = $peak_alignment.max_align_mz_diff,
+                match_tol_ppm = $history_db.match_tol_ppm,
+                new_feature_min_count = $history_db.new_feature_min_count,
+                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 = $weak_signal_recovery.recover_min_count,
+                cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
+            )
+        ]]></configfile>
+    </configfiles>
+
+    <expand macro="inputs">
+        <expand macro="history_db"/>
+        <expand macro="noise_filtering"/>
+        <expand macro="feature_detection"/>
+        <expand macro="peak_alignment"/>
+        <expand macro="weak_signal_recovery"/>
+        <expand macro="output_format"/>
+    </expand>
+
+    <outputs>
+        <expand macro="unsupervised_outputs"/>
+        <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
+        <data name="feature_known_table_pairing" format="tabular"
+              label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="known_table" value="known_table.parquet" ftype="parquet"/>
+            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
+            <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet"
+                    ftype="parquet"/>
+        </test>
+        <test>
+            <param name="known_table" value="known_table.parquet" ftype="parquet"/>
+            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
+            <section name="output_format">
+                <param name="out_format" value="recetox"/>
+            </section>
+            <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            @HELP_hybrid@
+        ]]>
+    </help>
+
+    <expand macro="citations"/>
+</tool>