--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_strain_profiler.xml	Wed May 12 09:03:21 2021 +0000
@@ -0,0 +1,68 @@
+<tool id="humann_strain_profiler" name="Make strain profiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+humann_strain_profiler
+    --input '$input'
+    --critical_mean $critical_mean
+    --critical_count $critical_count
+    --pinterval $pinterval_1 $pinterval_2
+    --critical_samples $critical_samples
+#if str($limit) != ''
+    --limit '$limit'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular,biom1" label="Merged gene families output for two or more samples"/>
+        <param argument="--critical_mean" type="float" value="10.0" label="Default mean non-zero gene abundance for inclusion"/>
+        <param argument="--critical_count" type="integer" value="500" label="Default non-zero number of genes for inclusion"/>
+        <param name="pinterval_1" type="float" value="1e-10" label="Low prevalence threshold" help="Only genes with prevalence higher than the threshold are allowed"/>
+        <param name="pinterval_2" type="float" value="1" label="High prevalence threshold" help="Only genes with prevalence lower than the threshold are allowed"/>
+        <param argument="--critical_samples" type="integer" value="2" label="Threshold number of samples having strain"/>
+        <param argument="--limit" type="text" value="" optional="true" label="Limit output to species matching a particular pattern?" help="e.g. 'Streptococcus'"/>
+    </inputs>
+    <outputs>
+        <collection name="output" type="list">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)-strain_profile.tsv" format="tabular" directory="."/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="strain_profiler-input.txt"/>
+            <param name="critical_mean" value="1"/>
+            <param name="critical_count" value="2"/>
+            <param name="pinterval_1" value="1e-10"/>
+            <param name="pinterval_2" value="1"/>
+            <param name="critical_samples" value="2"/>
+            <output_collection name="output" type="list">
+                <element name="s1" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="A|g1.s1"/>
+                        <has_text text="10.0"/>
+                        <has_n_columns n="4"/>
+                    </assert_contents>
+                </element>
+                <element name="s2" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="A|g1.s2"/>
+                        <has_text text="10.0"/>
+                        <has_n_columns n="4"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This tool makes strain profiles, based on the principle of detecting variable 
+presence and absence of gene families within a species
+that is otherwise well-covered in multiple samples.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>