Mercurial > repos > recetox > ramclustr_csv

diff ramclustr_csv.xml @ 3:61035548f46c draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
author recetox
date Mon, 07 Jun 2021 15:13:41 +0000
parents 08b09930cd73
children
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line diff
--- a/ramclustr_csv.xml	Thu Feb 04 11:34:59 2021 +0000
+++ b/ramclustr_csv.xml	Mon Jun 07 15:13:41 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy0">
+<tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy1">
     <macros>
         <import>ramclustr_macros.xml</import>
     </macros>
@@ -11,6 +11,7 @@
         <expand macro="parameters_csv" />
         <expand macro="parameters_required" />
         <expand macro="parameters_optional_csv" />
+        <expand macro="parameters_optional_metadata" />
     </inputs>
 
     <command detect_errors="aggressive"><![CDATA[
@@ -44,6 +45,9 @@
                 #if $optional.fftempdir
                     fftempdir = $optional.fftempdir,
                 #end if
+                #if $metadata.batch_order_qc
+                    metadata = "$metadata.batch_order_qc"
+                #end if
                 )'
             -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
 
@@ -59,7 +63,7 @@
 
     <tests>
         <test>
-            <param name="ms" value="csv_test-input.csv" ftype="csv"/>
+            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
             <param name="sample_name_column" value="1"/>
             <param name="feature_delimiter" value="_"/>
             <param name="retention_time_column" value="2"/>
@@ -81,11 +85,24 @@
             <param name="replace_zeros" value="True"/>
             <param name="Merge MSP Files" value="True"/>
             <param name="maxt" value="1"/>
-            <output name="result" file="ramclustR-csv_object.RData"/>
-            <output name="spec_abundance" file="spec-abundance_csv.csv" ftype="csv"/>
-            <output name="method_metadata" file="metadata_csv.txt" ftype="txt"/>
+            <output name="result" file="ramclustObj_csv_1.rdata"/>
+            <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
+            <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
             <output_collection name="mass_spectra" type="list">
-                <element name="fill" file="test-spectra_csv.msp" ftype="msp"/>
+                <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
+            <param name="sample_name_column" value="1"/>
+            <param name="feature_delimiter" value="_"/>
+            <param name="retention_time_column" value="2"/>
+            <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
+            <output name="result" file="ramclustObj_csv_2.rdata"/>
+            <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
+            <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
+            <output_collection name="mass_spectra" type="list">
+                <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
             </output_collection>
         </test>
     </tests>