--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shuffle_predictions.xml	Sat Mar 04 20:28:14 2023 +0000
@@ -0,0 +1,91 @@
+<tool id="picrust2_shuffle_predictions" name="PICRUSt2 Generation of shuffled predictions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>for a specified number of replicates</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tool"/>
+    <expand macro="requirements"/>
+    <version_command>shuffle_predictions.py -v</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '$input' predicted.tsv &&
+shuffle_predictions.py
+    --input predicted.tsv
+    --outdir predicted_shuffled
+    --rep $rep
+#if str($seed) != ''
+    --seed $seed
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular" label="Input prediction table"/>
+        <param argument="--rep" type="integer" min="1" value="1" label="Number of shuffled replicates to create"/>
+        <param argument="--seed" type="integer" optional="true" label="Random seed" help="Set this for reproducible shufflings"/>
+    </inputs>
+    <outputs>
+        <collection name="predicted_shuffled" type="list">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="predicted_shuffled/" format="tabular"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="EC_predicted.tsv.gz"/>
+            <param name="rep" value="5"/>
+            <param name="seed" value="131"/>
+            <output_collection name="predicted_shuffled" type="list" count="5">
+                <element name="predicted_shuf1.tsv" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="8db33d54e5184b0f448ae140f793368a"/>
+                        <has_n_lines n="38"/>
+                    </assert_contents>
+                </element>
+                <element name="predicted_shuf2.tsv" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="763af2e6cfd1d573893fa6d28aafc4b5"/>
+                        <has_n_lines n="38"/>
+                    </assert_contents>
+                </element>
+                <element name="predicted_shuf3.tsv" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="f5b23f626e3f2d2d1213f83c6de3e385"/>
+                        <has_n_lines n="38"/>
+                    </assert_contents>
+                </element>
+                <element name="predicted_shuf4.tsv" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="ff33233ffebbe6e3720af8bba7e89f08"/>
+                        <has_n_lines n="38"/>
+                    </assert_contents>
+                </element>
+                <element name="predicted_shuf5.tsv" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="691eeed271e420c8e7a91d5ea0cf5431"/>
+                        <has_n_lines n="38"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Generating shuffled predictions
+===============================
+Shuffles sequence ids of prediction table for a specified number of replicates.
+
+Note
+====
+This means that the prediction table is not totally scrambled across all colunmns: each predicted genome is still the same, but the sequence ids (e.g. the ASV id) linked with each predicted genome is randomized.
+
+Input
+=====
+Prediction table
+
+Output
+======
+Predicted shuffled table
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41587-020-0548-6</citation>
+    </citations>
+</tool>
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