diff tools/myTools/12_extract_perts.xml @ 1:7e5c71b2e71f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/myTools/12_extract_perts.xml	Wed Dec 22 16:00:34 2021 +0000
@@ -0,0 +1,39 @@
+<tool id="netisce12" name="Netisce Step 12" version="0.1.0" python_template_version="3.5">
+<description>Extracts the combinations of perturbations on FVS control nodes that pass filtering criterion 2</description>
+
+    <requirements>
+        <requirement type="package" version="1.1.5">pandas</requirement>
+        <requirement type="package" version="3.5.0">sys</requirement>
+    </requirements>
+    
+    <command> python3 '$__tool_directory__/bin/get_perts.py' '$fvs_init' '$fvs' '$filtered_perts' </command>
+
+    <inputs>
+        <param name="fvs_init" type="data" format="txt" label="FVS perturbations initialization"/>
+        <param name="fvs" type="data" format="txt" label="Minimal Feedback Vertex Set"/>
+        <param name="filtered_perts" type="data" format="txt" label="list of perturbation IDs that passed filtering criterion 2. "/>
+
+    </inputs>
+
+    <outputs>
+        <data name="output" format="txt" from_work_dir="extracted_perts.txt" label="combinations of perturbations on FVS control nodes that pass filtering criterion 2."/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="fvs_init" value="init.txt"/>
+            <param name="fvs" value="fvs.txt"/>
+            <param name="filtered_perts" value="crit2_perturbations.txt"/>
+            <output name="output" value="extract_perts.txt" ftype="txt" />
+        </test>
+    </tests>
+
+    <help>
+    This tool extracts the combinations of perturbations on FVS control nodes that pass filtering criterion 2.
+    Required Inputs:
+    1. Random Perturbation States for Feedback Vertex Set
+    2. Feedback Vertex Set
+    3. Perturbation Attractors that successfully shifted the network from undesired to desired state
+    </help>
+
+</tool>
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