Mercurial > repos > iuc > ampvis2_heatmap

diff heatmap.xml @ 3:a2d4da20749a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
author iuc
date Mon, 26 Feb 2024 07:53:13 +0000
parents 1adde216bdce
children 14695ae019be
line wrap: on
line diff
--- a/heatmap.xml	Mon Dec 18 09:37:32 2023 +0000
+++ b/heatmap.xml	Mon Feb 26 07:53:13 2024 +0000
@@ -57,10 +57,9 @@
                 #if $sort_by_cond.sort_by_sel != 'no'
                     sort_by = "$sort_by_cond.sort_by",
                 #end if
-                ## TODO https://github.com/MadsAlbertsen/ampvis2/issues/130
-                ## #if $normalise_by_cond.normalise_by_sel != "no"
-                ##     normalise_by = "$normalise_by_cond.normalise_by",
-                ## #end if
+                #if $normalise_by
+                    normalise_by = "$normalise_by",
+                #end if
                 #if $scale_by
                     scale_by = "$scale_by",
                 #end if
@@ -151,8 +150,9 @@
                 </param>
             </when>
         </conditional>
-        <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130  -->
-        <!-- <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/> -->
+        <!-- https://github.com/KasperSkytte/ampvis2/issues/168 
+            if this is possible again reuse: metadata_sample_or_variable_select ? -->
+        <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
         <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>
 
         <conditional name="plot_functions_cond">
@@ -226,19 +226,15 @@
             <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf"/>
         </test>
         <!-- normalise by a specific sample -->
-        <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 -->
-        <!-- <test expect_num_outputs="1">
+        <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
             <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
             <param name="normalise" value="true"/>
-            <conditional name="normalise_by_cond">
-                <param name="normalise_by_sel" value="sample"/>
-                <param name="normalise_by" value="16SAMP-747"/>
-            </conditional>
+            <param name="normalise_by" value="16SAMP-747"/>
             <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf"/>
-        </test> -->
-        <!-- normalise by a metadata variable -->
-        <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 -->
+        </test>
+        <!-- normalise by a metadata variable
+            https://github.com/KasperSkytte/ampvis2/issues/168 -->
         <!-- <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
             <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>