comparison disruptin_finder.xml @ 1:b973bc75693d draft

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date Mon, 05 Jun 2023 02:40:49 +0000
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1 <tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1">
2 <description>finds proteins with size and charge criteria</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 python '$__tool_directory__/disruptin_finder.py'
10 '$fasta_file'
11 --thresh_net_charge '$thresh_net_charge'
12 --thresh_size '$thresh_size'
13 --thresh_charge_ratio '$thresh_charge_ratio'
14 --selection_criteria '$selection_criteria'
15
16 > '$output']]></command>
17 <inputs>
18 <param label="Fasta" name="fasta_file" type="data" format="fasta"/>
19 <param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4"/>
20 <param label="Maximum Length" name="thresh_size" type="integer" value="100"/>
21 <param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25"/>
22 <param type="select" label="Type of selection criteria" name="selection_criteria">
23 <option value="net">Net charge</option>
24 <option value="ratio">Ratio of charged residues to sequence length</option>
25 <option value="both" selected="true">Both net charge and ratio</option>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="fasta" name="output"/>
30 </outputs>
31 <help><![CDATA[
32 **What it does**
33 This program finds proteins sequences based on given selection criteria: net charge, sequence length,
34 and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences,
35 thresholds for size, charge, and charge-to-size ratio criteria.
36
37 This tool returns the selected sequences in a fasta format.
38
39 ]]></help>
40 <citations>
41 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
42 <citation type="bibtex">
43 @unpublished{galaxyTools,
44 author = {A. Holt},
45 title = {CPT Galaxy Tools},
46 year = {2020},
47 note = {https://github.com/tamu-cpt/galaxy-tools/}
48 }
49 </citation>
50 </citations>
51 </tool>