diff magnitude_difference_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/magnitude_difference_flags.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,98 @@
+<tool id="secimtools_magnitude_difference_flags" name="Magnitude Difference Flags" version="@WRAPPER_VERSION@">
+    <description>- Count the number of digits before the decimal place.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+magnitude_difference_flags.py
+--input $input
+--design $design
+--ID $uniqID
+--flags $flags
+--figure $figure
+--counts "counts"
+--html $html
+--htmlPath "$html.files_path"
+
+#if $nozero:
+    --noZero
+#end if
+#if $group:
+    --group $group
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique identifiers.."/>
+        <param name="nozero" type="select" size="30" display="radio" value="yes" label="Remove zeros before processing" help="If not removed, zeros may skew the results.">
+            <option value="yes">Remove zeros</option>
+            <option value="no">Do not remove zeros</option>
+        </param>
+        <param name="group" size="30" type="text" label="Group/Treatment [Optional]" help="Name of the column in your Design File that contains group classifications." />
+    </inputs>
+    <outputs>
+        <data format="pdf" name="figure"  label="${tool.name} on ${on_string}: Figure" />
+        <data format="tabular" name="flags" label="C${tool.name} on ${on_string}: Flags" />
+        <data format="html" name="html" label="${tool.name} on ${on_string}: Counts" />
+    </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" />
+            <param name="nonzero" value="yes" />
+            <output name="figure" file="ST000006_magnitude_difference_flags_figure.pdf" compare="sim_size" delta="10000"/>
+            <output name="flags"  file="ST000006_magnitude_difference_flags_flags.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+This tool counts the number of digits before the decimal place for each feature in each sample.
+The tool identifies features with different orders of magnitude across different samples in a given group and produces corresponding indicator flags.
+Unusual samples are identified by finding systematically low or high feature values for that particular sample.
+
+--------------------------------------------------------------------------------
+
+**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@
+
+**Remove zeros before processing**
+
+  - If zeros are not removed before processing, they may skew the results.
+
+@GROUP_OPTIONAL@
+
+**NOTE:** Groups with one element will be excluded from the test.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The tool outputs a variable number of files (from 2 to n+1) depending on the number of groups (n).
+
+(1) TSV file containing a 0/1 indicator flag where “1” is used to flag features where the difference in the digit counts is greater than 2.
+
+(2) TSV file containing the digit counts for all samples or for the samples within groups,  depending on whether the Group/Treatment [Optional] parameter was provided.
+
+(3) A PDF file of the distribution of digit counts within each group of samples.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>