Mercurial > repos > recetox > recetox_aplcms_unsupervised

diff recetox_aplcms_unsupervised.xml @ 10:6057540f65a9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
author recetox
date Thu, 21 Oct 2021 15:03:18 +0000
parents b18c2d014b28
children e0f77e03599e
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line diff
--- a/recetox_aplcms_unsupervised.xml	Tue Oct 05 13:12:50 2021 +0000
+++ b/recetox_aplcms_unsupervised.xml	Thu Oct 21 15:03:18 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy1">
+<tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy2">
     <description>generate a feature table from LC/MS spectra</description>
     <macros>
         <import>recetox_aplcms_macros.xml</import>
@@ -22,6 +22,7 @@
                 sample_files = c('$filenames_str'),
                 aligned_file = '${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,
@@ -55,6 +56,7 @@
         <expand macro="feature_detection" />
         <expand macro="peak_alignment" />
         <expand macro="weak_signal_recovery" />
+        <expand macro="output_format" />
     </expand>
 
     <outputs>
@@ -66,6 +68,13 @@
             <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
             <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet"/>
         </test>
+        <test>
+            <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="unsupervised.recetox.parquet" ftype="parquet"/>
+        </test>
     </tests>
 
     <help>