changeset 9:a39431460e70 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viz.xml	Fri Oct 16 18:17:03 2020 +0000
@@ -0,0 +1,54 @@
+<tool id="viz_tool" name="Viz_tool: After Deseq2" version="0.1.0">
+  <description>for each sequence in a file</description>
+  <requirements>
+    <requirement type="package" version="1.7">fpdf</requirement>
+    <requirement type="package" version="3.7.4">python</requirement>
+    <requirement type="package" version="1.17.3">numpy</requirement>
+    <requirement type="package" version="3.1.2">matplotlib</requirement>
+    <requirement type="package" version="1.0.3">pandas</requirement>
+  </requirements>
+  <command>
+    #if $stats.choice == "1":
+      python $__tool_directory__/viz_ultra.py -in $input_file -p_value "$stats.pvalue" -fc $log2fc -top $top_mirna -tool_dir $__tool_directory__ -statistic "$stats.choice" -diff_tool "$tool"
+    #else:
+      python $__tool_directory__/viz_ultra.py -in $input_file -p_value "$stats.padj" -fc $log2fc -top $top_mirna -tool_dir $__tool_directory__ -statistic "$stats.choice" -diff_tool "$tool"
+    #end if
+  </command>
+  <inputs>
+    <param name="tool" type="select" label="File comes from" help="Choose the tool which generates the input file.">
+      <option value="1" selected="true">Deseq2</option>
+      <option value="2">EdgeR</option>
+    </param>
+    <param name="input_file" type="data" format="tabular" label="Input file" help="File from Deseq2 or EdgeR"/>
+    <param name="top_mirna" type="select" label="Choose the top differentially miRNAs of the analysis" help="Choose the number of top differentially expressed miRNAs.">
+      <option value="10" selected="true">Top 10</option>
+      <option value="20">Top 20</option>
+      <option value="30">Top 30</option>
+      <option value="40">Top 40</option>
+      <option value="50">Top 50</option>
+    </param>
+    <conditional name="stats">
+     <param name="choice" type="select" label="Choose p-value or p-adj" help="asdadadasd">
+      <option value="1" selected="true">Pvalue</option>
+      <option value="2">Padj</option>
+     </param>
+     <when value="1">
+      <param name="pvalue" type="float" min="0" max="1" value="0.05" label="P-value (max value)" help="p-value threshold" />
+     </when>
+     <when value="2">
+      <param name="padj" type="float" min="0" max="1" value="0.05" label="P-adjustment (max value)" help="p-adjustment threshold" />
+     </when>
+    </conditional>
+    <param name="log2fc" type="float" min="0" max="10" value="1" label="Log2FC (Absolute value)" help="Log2FC threshold" />
+  </inputs>
+  <outputs>
+    <!--data name="TOP_temp" format="png" label="TOP_$top_mirna Differentially Expressed miRNAs" from_work_dir="$__tool_directory__/tem.png" /-->
+    <!--data name="TOP_non" format="png" label="TOP_$top_mirna Differentially Expressed miRNAs" from_work_dir="$__tool_directory__/non.png" /-->
+    <data name="Scatter" format="png" label="Scatter Differentially Expressed miRNAs" from_work_dir="$__tool_directory__/a3.png" />
+    <data name="File" format="pdf" label="PDF" from_work_dir="$__tool_directory__/report2.pdf" />
+    <data name="File1" format="txt" label="txt" from_work_dir="$__tool_directory__/demo.txt" />
+  </outputs>
+  <help>
+
+  </help>
+</tool>