1
|
1 <tool id="netisce1" name="Netisce Step 1" version="0.1.0" python_template_version="3.5">
|
|
2
|
|
3 <description>Estimates attractors from experimental data using Signal Flow Analysis.</description>
|
|
4
|
|
5 <requirements>
|
|
6 <requirement type="package" version="3.5.0">os</requirement>
|
|
7 <requirement type="package" version="1.19.5">numpy</requirement>
|
|
8 <requirement type="package" version="1.1.5">pandas</requirement>
|
|
9 <requirement type="package" version="1.11.0">networkx</requirement>
|
|
10 <requirement type="package" version="3.5.0">random</requirement>
|
|
11 <requirement type="package" version="3.1.14">sfa</requirement>
|
|
12 <requirement type="package" version="3.5.0">csv</requirement>
|
|
13 <requirement type="package" version="3.5.0">sys</requirement>
|
|
14 </requirements>
|
|
15
|
|
16 <command>python3 '$__tool_directory__/bin/SFA_exp_attr.py' '$network' '$expression_data' exp_attrs.csv</command>
|
|
17
|
|
18 <inputs>
|
|
19 <param name="network" type="data" format="sif" label="Network"/>
|
|
20 <param name="expression_data" type="data" format="csv" label="Expression Data"/>
|
|
21 </inputs>
|
|
22
|
|
23 <outputs>
|
|
24 <data name="output" format="tabular" from_work_dir="attrs_exp.tsv" label="Experimental Attractors"/>
|
|
25 </outputs>
|
|
26
|
|
27 <tests>
|
|
28 <test expect_num_outputs="1">
|
|
29 <param name="network" value="network.sif" />
|
|
30 <param name="expression_data" value="expressions.csv" />
|
|
31 <output name="output" file="attrs_exp.tsv" ftype="tsv" />
|
|
32 </test>
|
|
33 </tests>
|
|
34
|
|
35 <help>
|
|
36 This tool estimates attractors for each experimental sample from normalized expression data using Signal Flow Analysis.
|
|
37 Required Inputs:
|
|
38 1. network in sif format (activating edges as "activates", inhibitory edges as "inhibits")
|
|
39 2. normalized expression values for data sample
|
|
40 </help>
|
|
41
|
|
42 <citations>
|
|
43 <citation type="doi">10.1038/s41598-019-50790-0</citation>
|
|
44 </citations>
|
|
45 </tool> |