Mercurial > repos > cpt > cpt_disruptin_finder
comparison cpt_disruptin_finder/disruptin_finder.xml @ 0:3f0d07a10405 draft
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author | cpt |
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date | Fri, 17 Jun 2022 12:22:15 +0000 |
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1 <?xml version="1.1"?> | |
2 <tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1"> | |
3 <description>finds proteins with size and charge criteria</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 <import>cpt-macros.xml</import> | |
7 </macros> | |
8 <expand macro="requirements"/> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 python $__tool_directory__/disruptin_finder.py | |
11 $fasta_file | |
12 --thresh_net_charge $thresh_net_charge | |
13 --thresh_size $thresh_size | |
14 --thresh_charge_ratio $thresh_charge_ratio | |
15 --selection_criteria $selection_criteria | |
16 | |
17 > $output]]></command> | |
18 <inputs> | |
19 <param label="Fasta" name="fasta_file" type="data" format="fasta" /> | |
20 <param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4" /> | |
21 <param label="Maximum Length" name="thresh_size" type="integer" value="100" /> | |
22 <param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25" /> | |
23 | |
24 <param type="select" label="Type of selection criteria" name="selection_criteria"> | |
25 <option value="net">Net charge</option> | |
26 <option value="ratio">Ratio of charged residues to sequence length</option> | |
27 <option value="both" selected="true">Both net charge and ratio</option> | |
28 </param> | |
29 | |
30 </inputs> | |
31 <outputs> | |
32 <data format="fasta" name="output"/> | |
33 </outputs> | |
34 <help><![CDATA[ | |
35 **What it does** | |
36 This program finds proteins sequences based on given selection criteria: net charge, sequence length, | |
37 and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences, | |
38 thresholds for size, charge, and charge-to-size ratio criteria. | |
39 | |
40 This tool returns the selected sequences in a fasta format. | |
41 | |
42 ]]></help> | |
43 <citations> | |
44 <citation type="doi">10.1371/journal.pcbi.1008214</citation> | |
45 <citation type="bibtex"> | |
46 @unpublished{galaxyTools, | |
47 author = {A. Holt}, | |
48 title = {CPT Galaxy Tools}, | |
49 year = {2020}, | |
50 note = {https://github.com/tamu-cpt/galaxy-tools/} | |
51 } | |
52 </citation> | |
53 </citations> | |
54 </tool> |