diff humann_renorm_table.xml @ 0:f76163304dab draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_renorm_table.xml	Mon Feb 13 16:21:18 2023 +0000
@@ -0,0 +1,83 @@
+<tool id="humann_renorm_table" name="Renormalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+    <description>a 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_renorm_table
+    --input '$input'
+    -o '$output'
+    --units '$units'
+    --mode '$mode'
+    --special '$special'
+    $update_snames
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
+        <param argument="--units" type="select" label="Normalization scheme">
+            <option value="cpm" selected="true">Copies per million</option>
+            <option value="relab">Relative abundance</option>
+        </param>
+        <param argument="--mode" type="select" label="Normalization level">
+            <option value="community" selected="true">Normalization of all levels by community total</option>
+            <option value="levelwise">Normalization of all levels by levelwise total</option>
+        </param>
+        <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
+        <param argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="demo_pathabundance.tsv"/>
+            <param name="units" value="cpm"/>
+            <param name="mode" value="community"/>
+            <param name="special" value="n"/>
+            <param name="update_snames" value=""/>
+            <output name="output" ftype="tabular" file="cpm_community_renormalized_pathway_abundance.tsv">
+                <assert_contents>
+                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis" />
+                    <has_text text="578694" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="demo_pathabundance.tsv"/>
+            <param name="units" value="relab"/>
+            <param name="mode" value="levelwise"/>
+            <param name="special" value="y"/>
+            <param name="update_snames" value=""/>
+            <output name="output" ftype="tabular" file="relab_levelwise_renormalized_pathway_abundance.tsv">
+                <assert_contents>
+                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified" />
+                    <has_text text="0.630281" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+HUMAnN quantifies genes and pathways in units of RPKs (reads per kilobase). These account for gene length but not sample sequencing depth. 
+While there are some applications, e.g. strain profiling, where RPK units are superior to depth-normalized units, most of the 
+time a user will renormalize their samples prior to downstream analysis.
+
+This tool provides the choice to normalize to relative abundance or copies per million (CPM) units. Both of these represent 
+"total sum scaling (TSS)"-style normalization: in the former case, each sample is constrained to sum to 1, whereas in the 
+latter case (CPMs) samples are constrained to sum to 1 million. Units out of 1 million are often more convenient for tables
+with many, many features (such as genefamilies.tsv tables).
+
+Note: CPM as used here does not refer to unnormalized COUNTS per million, but rather copies per million.
+CPMs as used here are a generic analog of the TPM (transcript per million) unit in RNA-seq. You may wish to use the 
+abbreviation CoPM for added clarity.
+
+By default, this tool normalizes all stratification levels to the sum of all community feature totals, but other options 
+(such as level-wise normalization) are supported. "Special" features (such as UNMAPPED) can be included or excluded in the 
+normalization process.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>