diff combine_metaphlan2_humann2.xml @ 0:31394a0c0242 draft

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combine_metaphlan2_humann2.xml	Fri Apr 15 09:15:21 2016 -0400
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+<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0">
+    <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 $type    
+
+            #if str($type) == 'gene_families'
+                --output_file $gene_families_output_file
+            #else
+                --output_file $pathway_output_file
+            #end if
+    ]]></command>
+
+    <inputs>
+        <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
+        
+        <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>
+
+        <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
+            <option value="gene_families" selected="true">Gene families</option>
+            <option value="pathways">Pathways</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="gene_families_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
+            <filter>type=="gene_families"</filter>
+        </data>
+        <data name="pathway_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" >
+            <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"/>
+    	</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"/>
+    	</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.
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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