# HG changeset patch
# User iuc
# Date 1639843513 0
# Node ID 5b5373005fbb2f46dc63961e3975805bd0276c16
# Parent  6b9977a09f6a2ae79c791d816feced589d55971b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"

diff -r 6b9977a09f6a -r 5b5373005fbb compare_biom.xml
--- a/compare_biom.xml	Thu Nov 28 20:43:10 2019 +0000
+++ b/compare_biom.xml	Sat Dec 18 16:05:13 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0">
+<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@TOOL_VERSION@.1">
     <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description>
     <macros>
         <import>macros.xml</import>
@@ -10,33 +10,33 @@
             -e '$expected'
             -o '$outfile'
             $not_relative_abundance_scores
+            $advanced.compare_observations
             $advanced.normalize
             $advanced.limit_to_observed_observations
             $advanced.limit_to_expected_observations
             $advanced.shuffle_samples
-
             '$observed'
     ]]></command>
     <inputs>
-        <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>
-        <param name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>
-        <param argument="not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"
+        <param argument="-o" name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>
+        <param argument="-e" name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>
+        <param argument="--not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"
                help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/>
         <section name="advanced" title="Advanced parameters" expanded="false">
-            <param argument="compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"
+            <param argument="--compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"
                 help="Calculate accuracy values by comparing between observations (instead of between samples)."/>
-            <param argument="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"
+            <param argument="--normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"
                 help="Convert both expected and observed tables to relative abundances (instead of observations)."/>
-            <param argument="limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"
+            <param argument="--limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"
                 help="Ignore observations that are not in the observed table."/>
-            <param argument="limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"
+            <param argument="--limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"
                 help="Ignore observations that are not in the expected table."/>
-            <param argument="shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?"
+            <param argument="--shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?"
                 help="Shuffle samples ids randomly before measuring accuracy."/>
         </section>
     </inputs>
     <outputs>
-        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} Comparison summary"/>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test><!-- relative abundance test -->
@@ -48,38 +48,71 @@
                     <has_text text="sample1"/>
                     <has_text text="sample3"/>
                     <has_text text="sample2"/>
+                    <has_n_lines n="4"/>
+                    <has_n_columns n="16"/>
                 </assert_contents>
             </output>
+            <assert_command>
+                <not_has_text text="--not_relative_abundance_scores"/>
+                <not_has_text text="--compare_observations"/>
+                <not_has_text text="--normalize"/>
+                <not_has_text text="--limit_to_observed_observations"/>
+                <not_has_text text="--limit_to_expected_observations"/>
+                <not_has_text text="--shuffle_samples"/>
+            </assert_command>
         </test>
         <test><!-- real counts test -->
             <param name="observed" value="observed.biom" ftype="biom1"/>
             <param name="expected" value="expected.biom" ftype="biom1"/>
-            <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>
+            <param name="not_relative_abundance_scores" value="true"/>
             <output name="outfile" ftype="tabular">
                 <assert_contents>
                     <has_text_matching expression="file\tlabel\taccuracy"/>
                     <has_text text="sample1"/>
                     <has_text text="sample3"/>
                     <has_text text="sample2"/>
+                    <has_n_lines n="4"/>
+                    <has_n_columns n="16"/>
                 </assert_contents>
             </output>
+            <assert_command>
+                <has_text text="--not_relative_abundance_scores"/>
+                <not_has_text text="--compare_observations"/>
+                <not_has_text text="--normalize"/>
+                <not_has_text text="--limit_to_observed_observations"/>
+                <not_has_text text="--limit_to_expected_observations"/>
+                <not_has_text text="--shuffle_samples"/>
+            </assert_command>
         </test>
         <test><!-- all other switches test -->
             <param name="observed" value="observed.biom" ftype="biom1"/>
             <param name="expected" value="expected.biom" ftype="biom1"/>
-            <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>
-            <param name="compare_observations" value="--compare_observations"/>
-            <param name="normalize" value="--normalize"/>
-            <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/>
-            <param name="shuffle_samples" value="--shuffle_samples"/>
+            <param name="not_relative_abundance_scores" value="true"/>
+            <section name="advanced">
+                <param name="compare_observations" value="true"/>
+                <param name="normalize" value="true"/>
+                <param name="limit_to_observed_observations" value="true"/>
+                <param name="limit_to_expected_observations" value="true"/>
+                <param name="shuffle_samples" value="true"/>
+            </section>
             <output name="outfile" ftype="tabular">
                 <assert_contents>
                     <has_text_matching expression="file\tlabel\taccuracy"/>
-                    <has_text text="sample1"/>
-                    <has_text text="sample3"/>
-                    <has_text text="sample2"/>
+                    <has_text text="K00005"/>
+                    <has_text text="K00004"/>
+                    <has_text text="K00003"/>
+                    <has_n_lines n="6"/>
+                    <has_n_columns n="16"/>
                 </assert_contents>
             </output>
+            <assert_command>
+                <has_text text="--not_relative_abundance_scores"/>
+                <has_text text="--compare_observations"/>
+                <has_text text="--normalize"/>
+                <has_text text="--limit_to_observed_observations"/>
+                <has_text text="--limit_to_expected_observations"/>
+                <has_text text="--shuffle_samples"/>
+            </assert_command>
         </test>
     </tests>
     <help>
diff -r 6b9977a09f6a -r 5b5373005fbb macros.xml
--- a/macros.xml	Thu Nov 28 20:43:10 2019 +0000
+++ b/macros.xml	Sat Dec 18 16:05:13 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">1.1.1</token>
+    <token name="@TOOL_VERSION@">1.1.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.1.1">picrust</requirement>
@@ -77,7 +77,7 @@
 For more information please visit:
 
 - PICRUSt Documentation: https://picrust.github.io/picrust/
-- PICRUSt GitHub: http://picrust.github.com/
+- PICRUSt GitHub: https://github.com/picrust/picrust/
 - PICRUSt Support: https://groups.google.com/d/forum/picrust-users
 
 **Reference Data**