diff humann_associate.xml @ 0:10fdefbf5920 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_associate.xml	Wed May 12 09:05:51 2021 +0000
@@ -0,0 +1,77 @@
+<tool id="humann_associate" name="Perform metadata association" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>on HUMAnN generated table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+humann_associate
+    --input '$input'
+    --focal-metadatum '$focal_metadatum'
+    --last-metadatum '$last_metadatum'
+    --focal-type '$focal_type'
+    --fdr $fdr
+    --output '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular" label="Gene family or pathway table with metadata rows at the top"/>
+        <param argument="--focal-metadatum" type="text" value="" label="Metadatum to test vs. community feature totals">
+            <sanitizer invalid_char="">
+                <valid initial="string.ascii_letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="empty_field" />
+        </param>
+        <param argument="--last-metadatum" type="text" value="" label="End of metadata rows">
+            <sanitizer invalid_char="">
+                <valid initial="string.ascii_letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="empty_field" />
+        </param>
+        <param name="focal_type" argument="--focal-type" type="select" label="Metadatum type">
+            <option value="continuous">Continuous</option>
+            <option value="categorical">Categorical</option>
+        </param>
+        <param argument="--fdr" type="float" value="0.2" label="FDR threshold"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="hmp_pathabund.txt"/>
+            <param name="focal_metadatum" value="STSite"/>
+            <param name="last_metadatum" value="STSite"/>
+            <param name="focal_type" value="categorical"/>
+            <param name="fdr" value="0.2"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Feature"/>
+                    <has_text text="BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis"/>
+                    <has_text text="Level means (|ed)"/>
+                    <has_text text="P-value"/>
+                    <has_text text="Q-value"/>
+                    <has_n_columns n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+When associating metadata with HUMAnN features, it is often beneficial to associate with community totals and avoid testing each 
+individual feature stratification (to improve statistical power).
+
+This is the approach used by this tool, which can compare feature totals across samples with 
+1) a single continuous metadatum (via the Spearman Correlation) or 
+2) a single categorical metadatum (via the Kruskal-Wallis H-test).
+
+Notably, this is a naive approach to association, but it is useful for tutorial purposes.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>