Mercurial > repos > laurenmarazzi > netisce_test
comparison tools/myTools/3_insilico_attrs.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="netisce3" name="Netisce Step 3" version="0.1.0" python_template_version="3.5"> | |
2 <description>Estimates the attractors for randomly generated initial states using signal flow analysis</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="1.1.5">pandas</requirement> | |
6 <requirement type="package" version="1.19.5">numpy</requirement> | |
7 <requirement type="package" version="3.5.0">os</requirement> | |
8 <requirement type="package" version="1.11.0">networkx</requirement> | |
9 <requirement type="package" version="3.5.0">random</requirement> | |
10 <requirement type="package" version="3.5.0">sys</requirement> | |
11 <requirement type="package" version="3.5.0">csv</requirement> | |
12 <requirement type="package" version="3.1.14">sfa</requirement> | |
13 <requirement type="package" version="1.0.3">statistics</requirement> | |
14 </requirements> | |
15 | |
16 <command>python3 '$__tool_directory__/bin/SFA_insilico.py' '$network' '$expression_data' '$samples' '$num_states'</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 <param name="samples" type="data" format="txt" label="Name of Experimental Samples"/> | |
22 <param name="num_states" type="integer" value="10000" label="Num of Insilico Attractors to Generate"/> | |
23 </inputs> | |
24 | |
25 <outputs> | |
26 <data name="output" format="tabular" from_work_dir="attrs_insilico.tsv" label="Insilico Attractors"/> | |
27 </outputs> | |
28 | |
29 <tests> | |
30 <test> | |
31 <param name="network" value="network.sif" /> | |
32 <param name="expression_data" value="expressions.csv" /> | |
33 <param name="num_states" value="10000"/> | |
34 <param name="samples" value="samples.txt" /> | |
35 <output name="output" file="attrs_insilico.tsv" ftype="tsv" /> | |
36 </test> | |
37 </tests> | |
38 | |
39 <help> | |
40 This tool estimates the attractors for randomly generated initial states using signal flow analysis. | |
41 Required Inputs: | |
42 1. network in sif format (activating edges as "activates", inhibitory edges as "inhibits") | |
43 2. normalized expression values for data sample | |
44 3. experimental sample names of interest | |
45 4. number of insilico Attractors to generate (default = 10,000) | |
46 </help> | |
47 | |
48 <citations> | |
49 <citation type="doi">10.1038/s41598-019-50790-0</citation> | |
50 </citations> | |
51 | |
52 </tool> |