--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_humann2_output.xml	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,86 @@
+<tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0">
+    <description>and extract information</description>
+
+    <requirements>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        mkdir specifics 
+        &&
+
+        python $__tool_directory__/compare_humann2_output.py
+            #for $sample in $samples:
+                --sample_name "${sample.sample_name}"
+                --charact_input_file "${sample.input}"
+                --specific_output_file "specifics/specific_to_${sample.sample_name}.txt"
+            #end for
+
+            --most_abundant_characteristics_to_extract $charact_nb
+            --more_abundant_output_file $more_abundant_output_file
+            --similar_output_file $similar_output_file
+            > $log
+                
+    ]]></command>
+
+    <inputs>
+        <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
+            <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/>
+            <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/>
+        </repeat>
+
+        <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/>
+    </inputs>
+
+    <outputs>
+        <data name="more_abundant_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
+        <data name="similar_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
+        <data name="log" format="txt"
+            label="${tool.name} on ${on_string}: Log" />
+        <collection name="specific_files" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
+        </collection>
+
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="samples_0|sample_name" value="sample1"/>
+            <param name="samples_0|input" value="humann2_m8_pathabundance_cmp_renormalized.tsv"/>
+            <param name="samples_1|sample_name" value="sample2"/>
+            <param name="samples_1|input" value="humann2_fasta_pathabundance_relab_renormalized.csv"/>
+            <param name="charact_nb" value="10"/>
+            <output name="more_abundant_output_file" file="more_abundant_output.tabular"/>
+            <output name="similar_output_file" file="similar_output.tabular"/>
+            <output name="log" file="log_output.txt"/>
+            <output_collection name="specific_files" type="list">
+                <element name="specific_to_sample1" file="specific_to_sample1_output.txt" />
+                <element name="specific_to_sample2" file="specific_to_sample2_output.txt" />
+            </output_collection>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
+
+  * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics
+
+  * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
+  
+  * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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