diff combine_metaphlan2_humann2.xml @ 1:e25efca0a49c draft

"planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"

--- a/combine_metaphlan2_humann2.xml	Fri Apr 15 09:15:21 2016 -0400
+++ b/combine_metaphlan2_humann2.xml	Mon Sep 14 12:19:49 2020 +0000
@@ -1,40 +1,32 @@
-<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0">
+<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.2.0">
     <description>to relate genus/species abundances and gene families/pathways abundances</description>
-
     <requirements>
     </requirements>
-
     <stdio>
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
-
     <version_command></version_command>
-
     <command><![CDATA[
         python $__tool_directory__/combine_metaphlan2_humann2.py 
-            --metaphlan2_file $metaphlan2_file
-            --humann2_file $humann2_file
-            --type $type    
+            --metaphlan2_fp '$metaphlan2_file'
+            --humann2_fp '$humann2_file'
+            --type '$type'   
 
             #if str($type) == 'gene_families'
-                --output_file $gene_families_output_file
+                --output_fp '$gene_families_output_file'
             #else
-                --output_file $pathway_output_file
+                --output_fp '$pathway_output_file'
             #end if
     ]]></command>
-
     <inputs>
         <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
-        
         <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>
-
         <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
             <option value="gene_families" selected="true">Gene families</option>
             <option value="pathways">Pathways</option>
         </param>
     </inputs>
-
     <outputs>
         <data name="gene_families_output_file" format="tabular"
             label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
@@ -45,30 +37,45 @@
             <filter>type=="pathways"</filter>
         </data>
     </outputs>
-
     <tests>
     	<test>
-    		 <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
-    		 <param name="humann2_file" value="humann2_gene_families_input.tabular"/>
-    		 <param name='type' value="gene_families"/>
-    		 <output name="gene_families_output_file" file="gene_families_output.tabular"/>
+    		<param name="metaphlan2_file" value="metaphlan2_input.txt"/>
+    		<param name="humann2_file" value="humann2_gene_families_input.tabular"/>
+    		<param name='type' value="gene_families"/>
+    		<output name="gene_families_output_file">
+                <assert_contents>
+                    <has_n_columns n="8"/>
+                    <has_n_lines n="29434"/>
+                    <has_text text="Staphylococcus_epidermidis"/>
+                    <has_text text="Putative transposon Tn552 DNA invertase bin3"/>
+                    <has_size value="3467947"/>
+                </assert_contents>
+            </output>
     	</test>
     	<test>
     		 <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
     		 <param name="humann2_file" value="humann2_pathways_input.tabular"/>
     		 <param name='type' value="pathways"/>
-    		 <output name="pathway_output_file" file="pathways_output.tabular"/>
+             <output name="pathway_output_file">
+                <assert_contents>
+                    <has_n_columns n="8"/>
+                    <has_n_lines n="1533"/>
+                    <has_text text="Rhodobacter_sphaeroides"/>
+                    <has_text text="superpathway of acetyl CoA biosynthesis"/>
+                    <has_size value="186363"/>
+                </assert_contents>
+            </output>
     	</test>
     </tests>
-
     <help><![CDATA[
 **What it does**
 
 This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs.
 
-For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus.
+For each gene families/pathways and the corresponding taxonomic stratification, 
+you get relative abundance of this gene family/pathway and the relative abundance 
+of corresponding species and genus.
     ]]></help>
-
     <citations>
     </citations>
 </tool>
\ No newline at end of file