Mercurial > repos > recetox > waveica

diff waveica.xml @ 2:6480c6d5fa36 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
author recetox
date Fri, 23 Jun 2023 07:27:29 +0000
parents b77023c41c76
children dbbedb14b44c
line wrap: on
line diff
--- a/waveica.xml	Thu Sep 29 15:21:04 2022 +0000
+++ b/waveica.xml	Fri Jun 23 07:27:29 2023 +0000
@@ -1,8 +1,9 @@
-<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy2" python_template_version="3.5">
+<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy3" python_template_version="3.5">
     <description>removal of batch effects for untargeted metabolomics data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="annotation"/>
     <expand macro="creator"/>
 
     <requirements>
@@ -19,6 +20,7 @@
                 #if $input_num.input_choice == "2":
                     metadata = "$input_num.input_metadata.metadata",
                     ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
+                    transpose = $input_num.transpose_feature_table,
                 #else:
                     ext = "$input_num.data.ext",
                 #end if
@@ -36,6 +38,7 @@
                 #if $input_num.input_choice == "2":
                     metadata = "$input_num.input_metadata.metadata",
                     ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
+                    transpose = $input_num.transpose_feature_table,
                 #else:
                     ext = "$input_num.data.ext",
                 #end if
@@ -61,10 +64,12 @@
                 <expand macro="input_data"/>
             </when>
             <when value="2">
+                <expand macro="input_data"/>
                 <section name="input_metadata" title="Input metadata table" expanded="true">
                     <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" />
-                </section> 
-                <expand macro="input_data"/>
+                </section>
+                <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false" 
+                truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />
             </when>
         </conditional>
         <expand macro="general_parameters"/>
@@ -93,7 +98,7 @@
             <param name="data" value="input_data.csv" ftype="csv"/>
             <param name="mode" value="batchwise"/>
             <param name="wavelet_filter" value="d"/>
-            <param name="filter_length" value="2"/>
+            <param name="wavelet_length" value="2"/>
             <param name="k" value="20"/>
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
@@ -104,7 +109,7 @@
             <param name="data" value="input_data.tsv" ftype="tsv"/>
             <param name="mode" value="batchwise"/>
             <param name="wavelet_filter" value="d"/>
-            <param name="filter_length" value="2"/>
+            <param name="wavelet_length" value="2"/>
             <param name="k" value="20"/>
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
@@ -115,7 +120,7 @@
             <param name="data" value="input_data.parquet" ftype="parquet"/>
             <param name="mode" value="batchwise"/>
             <param name="wavelet_filter" value="d"/>
-            <param name="filter_length" value="2"/>
+            <param name="wavelet_length" value="2"/>
             <param name="k" value="20"/>
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
@@ -128,7 +133,7 @@
             <param name="metadata" value="metadata.csv" ftype="csv"/>
             <param name="mode" value="batchwise"/>
             <param name="wavelet_filter" value="d"/>
-            <param name="filter_length" value="2"/>
+            <param name="wavelet_length" value="2"/>
             <param name="k" value="20"/>
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
@@ -141,7 +146,7 @@
             <param name="metadata" value="metadata.tsv" ftype="tsv"/>
             <param name="mode" value="batchwise"/>
             <param name="wavelet_filter" value="d"/>
-            <param name="filter_length" value="2"/>
+            <param name="wavelet_length" value="2"/>
             <param name="k" value="20"/>
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
@@ -154,13 +159,41 @@
             <param name="metadata" value="metadata.csv" ftype="csv"/>
             <param name="mode" value="batchwise"/>
             <param name="wavelet_filter" value="d"/>
-            <param name="filter_length" value="2"/>
+            <param name="wavelet_length" value="2"/>
             <param name="k" value="20"/>
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
             <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
         </test>
+        <test><!-- TEST 7 -->
+            <param name="input_choice" value="2"/>
+            <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
+            <param name="metadata" value="metadata.parquet" ftype="parquet"/>
+            <param name="transpose_feature_table" value="TRUE"/>
+            <param name="mode" value="batchwise"/>
+            <param name="wavelet_filter" value="d"/>
+            <param name="wavelet_length" value="2"/>
+            <param name="k" value="20"/>
+            <param name="t" value="0.05"/>
+            <param name="t2" value="0.05"/>
+            <param name="alpha" value="0"/>
+            <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
+        </test>
+        <test><!-- TEST 8 -->
+            <param name="input_choice" value="2"/>
+            <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
+            <param name="metadata" value="metadata.csv" ftype="csv"/>
+            <param name="transpose_feature_table" value="TRUE"/>
+            <param name="mode" value="batchwise"/>
+            <param name="wavelet_filter" value="d"/>
+            <param name="wavelet_length" value="2"/>
+            <param name="k" value="20"/>
+            <param name="t" value="0.05"/>
+            <param name="t2" value="0.05"/>
+            <param name="alpha" value="0"/>
+            <output name="normalized_data" file="normalized_data.csv"/>
+        </test>
         <!-- The following test has different results on three platform I've tried -->
         <!-- <test>
             <param name="data" value="input_data_nobatch.csv" ftype="csv"/>