diff coefficient_variation_flags.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coefficient_variation_flags.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,85 @@
+<tool id="secimtools_coefficient_variation_flags" name="Coefficient of Variation (CV) Flags" version="@WRAPPER_VERSION@">
+    <description>- Calculate the coefficient of variation and flag potential outliers.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+coefficient_variation_flags.py
+--input $input
+--design $design
+--ID $uniqID
+--figure $CVplot
+--flag $CVflag
+#if $group:
+    --group $group
+#end if
+#if $CVcutoff:
+    --CVcutoff $CVcutoff
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note: you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
+        <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications." />
+        <param name="CVcutoff"  type="float" optional="true" size="4" value="0.1" label="CV Cutoff [Optional]" help="The cutoff (in decimals) that specifies the proportion of features to flag.  The default CV cutoff is 0.1 which implies that 10% of the features with the largest CV-s will be flagged."/>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="CVplot"  label="${tool.name} on ${on_string}: Plot" />
+        <data format="tabular" name="CVflag"  label="${tool.name} on ${on_string}: Flag" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"   value="ST000006_data.tsv"/>
+            <param name="design"  value="ST000006_design.tsv"/>
+            <param name="uniqID"  value="Retention_Index" />
+            <param name="group"   value="White_wine_type_and_source" />
+            <output name="CVplot" file="ST000006_coefficient_variation_flags_with_group_figure.pdf" compare="sim_size" delta="100000"/>
+            <output name="CVflag" file="ST000006_coefficient_variation_flags_with_group_flag.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+This tool calculates the coefficient of variation (standard deviation as a percentage of the mean) and is often used to look at the consistency of features across samples.
+The user can define what percent of features with the highest CV to flag.
+If no percentage is selected, then the top 10% of features with the highest CV are flagged (default value of 0.1).
+The CV value corresponding to the percentage is given in the resulting histogram plot.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+
+@WIDE@
+
+**NOTE:** The sample IDs must match the sample IDs in the Design File (below).
+Extra columns will automatically be ignored.
+
+@METADATA@
+
+@UNIQID@
+
+**CV cutoff [Optional]**
+
+    - The cutoff (in decimals) that specifies the proportion of the features to flag.  The default CV cutoff is 0.1 which implies that 10% of the features with the largest CV will be flagged. If the Group/Treatment variable is provided, then the analysis is performed independently for each group. If no Group/Treatment variable is provided, the analysis is performed on the entire dataset.
+
+@GROUP_OPTIONAL@
+
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+This tool outputs two different files:
+
+(1) a TSV file containing the CV Flags for each feature for each group (if group variable is specified).  A flag value of one (1) corresponds to features with large CV values as specified by the CV cutoff.
+(2) a PDF file containing histograms with overlayed density plots of the coefficients of variation for each group (optional) and a summary density plot containing the densities for each group without the histograms.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>