diff distribution_samples.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/distribution_samples.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,85 @@
+<tool id="secimtools_distribution_samples" name="Generate Distribution of Features within Samples." version="@WRAPPER_VERSION@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+distribution_samples.py
+--input $input
+--design $design
+--ID $uniqID
+--figure $figure
+
+#if $group
+    --group $group
+#end if
+
+#if $order
+    --order $order
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique identifiers."/>
+        <param name="group" type="text" size="30" value="" optional="true" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications."/>
+        <param name="order" type="text" size="30" value="" optional="true" label="Run Order [Optional]" help="The column name in your design file that contains the order samples were run."/>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Plot"/>
+    </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="figure" file="ST000006_distribution_samples_with_group_figure.pdf" compare="sim_size" delta="10000"/>
+        </test>
+    </tests>
+<help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool plots the distribution of features within each sample.
+All samples are colored by group and are plotted on the same graph for comparison purposes.
+The distributions of the features within each sample are presented as estimated densities and box-and-whiskers plots with potential outliers.
+If the order samples were run is specified in the input, box plots will be displayed according to the run order.
+
+**NOTE:** This script works best with log transformed data.
+
+
+--------------------------------------------------------------------------------
+
+**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@
+
+@GROUP_OPTIONAL@
+
+@RUNORDER_OPTIONAL@
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+PDF file containing two plots:
+
+(1) Density plots illustrating the distribution of features within a given sample
+(2) Boxplots of the distribution of features within each sample
+
+]]></help>
+    <expand macro="citations"/>
+</tool>