diff add_group_rank.xml @ 2:caba07f41453 draft default tip

"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_group_rank.xml	Thu Jun 10 15:41:17 2021 +0000
@@ -0,0 +1,91 @@
+<tool id="secimtools_rank_group_wide" name="Ranked wide file"  version="@WRAPPER_VERSION@">
+    <description>Generate a wide format file with ranked columns from an input wide file.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+add_group_rank.py
+--wide $wide
+--design $design
+--out $out
+#if $ngroup:
+    --ngroup $ngroup
+#end if
+--uniqID $uniqID
+    ]]></command>
+    <inputs>
+        <param name="wide" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="rowID" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
+        <param name="ngroup" type="integer" size="30" value="" optional="true" label="number of groups for each feature being ranked" help="number of bins/groups for each feature being ranked. If there is no input, the default behavir is ranking each column."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Results Table"/>
+    </outputs>
+    <tests>
+      <test>
+	<param name="wide" value="ST000006_data.tsv"/>
+	<param name="design" value="ST000006_design.tsv"/>
+	<param name="uniqID" value="Retention_Index" />
+	<param name="ngroup" value="100" />
+	<output name="out" file="ST000006_add_group_rank_output_wide.tsv" />
+      </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool is used to generate a wide format file with each column being ranked in the input wide format dataset.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+    
+    An example of input wide file is like:
+
+        +---------+---------+---------+---------+-----+
+        | Feature | sample1 | sample2 | sample3 | ... |
+        +=========+=========+=========+=========+=====+
+        | one     | 10.2    | 20      | 10      | ... |
+        +---------+---------+---------+---------+-----+
+        | two     | 5.1     | 22      | 30      | ... |
+        +---------+---------+---------+---------+-----+
+        | three   | 30.5    | 27      | 2       | ... |
+        +---------+---------+---------+---------+-----+
+        | four    | 32.9    | 17      | 8       | ... |
+        +---------+---------+---------+---------+-----+
+        | ...     | ...     | ...     | ...     | ... |
+        +---------+---------+---------+---------+-----+
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The user will get a output file from the tool:
+
+- a wide format file with each column being ranked.
+
+The output wide file for the example above will be like:
+        
++---------+---------+---------+---------+-----+
+| Feature | sample1 | sample2 | sample3 | ... |
++=========+=========+=========+=========+=====+
+| one     | 2       | 2       | 3       | ... |
++---------+---------+---------+---------+-----+
+| two     | 1       | 3       | 4       | ... |
++---------+---------+---------+---------+-----+
+| three   | 3       | 4       | 1       | ... |
++---------+---------+---------+---------+-----+
+| four    | 4       | 1       | 2       | ... |
++---------+---------+---------+---------+-----+
+| ...     | ...     | ...     | ...     | ... |
++---------+---------+---------+---------+-----+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>