changeset 8:1a6cdf55390f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c

--- a/macros.xml	Wed Mar 29 08:00:24 2023 +0000
+++ b/macros.xml	Thu Apr 20 11:26:53 2023 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">4.0.6</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.05</token>
     <!-- Metaphlan DB compatible with this version of Metaphlan
     v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> 

--- a/metaphlan.xml	Wed Mar 29 08:00:24 2023 +0000
+++ b/metaphlan.xml	Thu Apr 20 11:26:53 2023 +0000
@@ -192,16 +192,18 @@
 mv 'bowtie2out' '$bowtie2out'
 #end if
 
-#if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
-&&
-mkdir 'split_levels'
-&&
-python '$__tool_directory__/formatoutput.py'
-    split_levels
-    --metaphlan_output '$output_file'
-    --outdir 'split_levels'
-    $out.legacy_output
 
+#if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats']
+    #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
+        &&
+        mkdir 'split_levels'
+        &&
+        python '$__tool_directory__/formatoutput.py'
+            split_levels
+            --metaphlan_output '$output_file'
+            --outdir 'split_levels'
+            $out.legacy_output
+    #end if
 #end if
 
 #if $out.krona_output
@@ -361,7 +363,7 @@
         <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
         <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
-            <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
+            <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
         </collection>
         <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
             <filter>out['krona_output']</filter>
@@ -435,8 +437,7 @@
                     <not_has_text text="p__Actinobacteria"/>
                 </assert_contents>
             </output>
-            <output_collection name="levels" type="list" >
-            
+            <output_collection name="levels" type="list">
                 <element name="all" ftype="tabular">
                     <assert_contents>
                         <has_text text="class"/>
@@ -1054,6 +1055,34 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Check a non-default analysis mode -->
+        <test expect_num_outputs="4">
+            <section name="inputs">
+                <conditional name="in">
+                    <param name="selector" value="raw"/>
+                    <conditional name="raw_in">
+                        <param name="selector" value="single"/>
+                        <param name="in" value="SRS014464-Anterior_nares.fasta"/>
+                    </conditional>
+                </conditional>
+                <conditional name="db">
+                    <param name="db_selector" value="cached"/>
+                    <param name="cached_db" value="test-db-20210409"/>
+                </conditional>
+            </section>
+            <section name="analysis">
+                <conditional name="analysis_type">
+                    <param name="t" value="marker_ab_table"/>
+                </conditional>
+            </section>
+            <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
+                <assert_contents>
+                    <has_text text="29394__H3NC06__B8A41_08715"/>
+                    <has_text text="SampleID"/>
+                    <has_text text="Metaphlan_Analysis"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 What it does