diff metaquantome_stat.xml @ 0:020a9ecdc1e1 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_stat.xml	Thu Apr 25 13:50:59 2019 -0400
@@ -0,0 +1,73 @@
+<tool id="metaquantome_stat" name="metaQuantome: stat" version="@GVERSION@">
+    <description>differential analysis of functional expression and taxonomic abundance</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        metaquantome stat
+        --samps '$samps'
+        --mode '$mode_args.mode'
+        #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
+            --ontology='$mode_args.ontology_args.ontology'
+        #end if
+        --file '$file'
+        --parametric '$parametric'
+        $paired
+        --outfile='$outfile'
+    ]]></command>
+    <inputs>
+        <expand macro="SAMPS"/>
+        <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
+                    help=""/>
+        <conditional name="mode_args">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="f">Functional analysis</option>
+                <option value="t">Taxonomic analysis</option>
+                <option value="ft">Functional-taxonomic interaction analysis</option>
+            </param>
+            <when value="f">
+                <expand macro="ONTOLOGY_ARGS"/>
+            </when>
+            <when value="t">
+            </when>
+            <when value="ft">
+                <expand macro="ONTOLOGY_ARGS"/>
+            </when>
+        </conditional>
+        <param argument="--parametric" type="select" label="Statistical test to perform">
+            <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
+            <option value="True">standard t-test (parametric)</option>
+        </param>
+        <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="file" value="ec_ttest.tab" ftype="tabular" />
+        <param name="parametric" value="True" />
+        <param name="ontology" value="ec" />
+        <param name="mode" value="f" />
+        <param name="samps" value="samples_basic.tab" ftype="tabular" />
+        <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
+      </test>
+    </tests>
+    <help><![CDATA[
+metaQuantome stat
+===================
+
+The *stat* module is the third step in the metaQuantome analysis workflow. The purpose
+of the *stat* module is to perform differential expression analysis between 2 experimental
+conditions. metaQuantome offers paired and unpaired tests,
+as well as parametric and non-parametric options.
+
+Questions, Comments, Problems, Kudos
+--------------------------------------
+
+Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>