Mercurial > repos > laurenmarazzi > netisce_test
comparison tools/myTools/1_sfa_exp.xml @ 1:7e5c71b2e71f draft default tip
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author | laurenmarazzi |
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date | Wed, 22 Dec 2021 16:00:34 +0000 |
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0:f24d4892aaed | 1:7e5c71b2e71f |
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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> |