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date Mon, 05 Jun 2023 02:51:59 +0000
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1 <tool id="edu.tamu.cpt2.spanin.generate-putative-usp" name="USP Candidates" version="1.0">
2 <description>constructs a putative list of potential u-spanin from an input genomic FASTA</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 </expand>
9 <command detect_errors="aggressive"><![CDATA[
10 python '$__tool_directory__/generate-putative-usp.py'
11 '$fa'
12 --strand '$strand'
13 --min_size '$min_size'
14 --max_size '$max_size'
15 --lipo_min_start '$lipo_min_start'
16 --lipo_max_start '$lipo_max_start'
17 --min_lipo_after '$min_lipo_after'
18 --max_lipo_after '$max_lipo_after'
19 --tmd_min_start '$tmd_min_start'
20 --tmd_max_start '$tmd_max_start'
21 --tmd_min_size '$tmd_min_size'
22 --tmd_max_size '$tmd_max_size'
23 --putative_usp_gff '$putative_usp_gff'
24 --summary_usp_txt '$summary_usp'
25 --putative_usp '$putative_usp'
26 --usp_og '$usp_og'
27 --usp_ob '$usp_ob'
28 --usp_op '$usp_op'
29 --usp_on '$usp_on'
30 --switch '$switch'
31 ]]></command>
32 <inputs>
33 <param label="FASTA" name="fa" type="data" format="fasta"/>
34 <param type="select" label="Strand Choice" name="strand">
35 <option value="both">both</option>
36 <option value="forward">+</option>
37 <option value="reverse">-</option>
38 </param>
39 <param label="u-spanin minimal length" type="integer" name="min_size" value="100"/>
40 <param label="u-spanin maximum length" type="integer" name="max_size" value="200"/>
41 <param label="Range Selection; default is all; slices are based on NT. Separated by a colon (eg. #:#)" name="switch" type="text" value="all"/>
42 <param label="TMD minimal distance from start codon" type="integer" name="tmd_min_start" value="75"/>
43 <param label="TMD maximum distance from start codon" type="integer" name="tmd_max_start" value="200"/>
44 <param label="TMD minimal size" type="integer" name="tmd_min_size" value="15"/>
45 <param label="TMD maximum size" type="integer" name="tmd_max_size" value="25"/>
46 <param label="Lipobox minimal distance from start codon" type="integer" name="lipo_min_start" value="10"/>
47 <param label="Lipobox maximum distance from start codon" type="integer" name="lipo_max_start" value="30"/>
48 <param label="Minimum amount of periplasmic residues after Lipobox" type="integer" name="min_lipo_after" value="60"/>
49 <param label="Maximum amount of periplasmic residues after Lipobox" type="integer" name="max_lipo_after" value="160"/>
50 </inputs>
51 <outputs>
52 <data format="fasta" name="usp_on" label="NucSequences.fa" hidden="true"/>
53 <data format="fasta" name="usp_op" label="ProtSequences.fa" hidden="true"/>
54 <data format="bed" name="usp_ob" label="BED_Output.bed" hidden="true"/>
55 <data format="gff3" name="usp_og" label="GFF_Output.gff" hidden="true"/>
56 <data format="fasta" name="putative_usp" label="putative_usp.fa"/>
57 <data format="txt" name="summary_usp" label="summary_usp.txt"/>
58 <data format="gff3" name="putative_usp_gff" label="putative_usp.gff3"/>
59 </outputs>
60 <tests>
61 <test>
62 <param name="fa" value="t1.fa"/>
63 <param name="min-size" value="100"/>
64 <param name="max-size" value="200"/>
65 <param name="switch" value="all"/>
66 <param name="tmd_min_start" value="75"/>
67 <param name="tmd_max_start" value="200"/>
68 <param name="tmd_min_size" value="15"/>
69 <param name="tmd_max_size" value="25"/>
70 <param name="lipo_min_start" value="15"/>
71 <param name="lipo_max_start" value="30"/>
72 <param name="min_lipo_after" value="60"/>
73 <param name="max_lipo_after" value="160"/>
74 <param name="select" value="1"/>
75 <output name="usp_on" file="_out_usp.fna"/>
76 <output name="usp_op" file="_out_usp.fa"/>
77 <output name="usp_ob" file="_out_usp.bed"/>
78 <output name="usp_og" file="_out_usp.gff3"/>
79 <output name="putative_usp" file="_putative_usp.fa"/>
80 <output name="summary_usp" file="_summary_usp.txt"/>
81 <output name="putative_usp_gff" file="_putative_usp.gff3"/>
82 </test>
83 </tests>
84 <help><![CDATA[
85
86 **What it does**
87 Searches a genome for candidate u-spanins (USPs), a phage protein involved in outer membrane disruption during Gram-negative bacterial host cell lysis.
88
89
90 **METHODOLOGY**
91 This tool combines the methods used in the ISP and OSP Candidates tools to search for putative transmembrane domains and lipoboxes. See those tools for additional detail. Within user-set parameters, the following residues are allowed:
92
93 Hydrophobic residues allowed in TMD:
94
95 * [FIWLVMYCATGSP]
96
97 Lipobox patterns:
98
99 * [ILMFTV][^REKD][GAS]C
100 * A W[AGS]C
101
102 **INPUT** --> Genomic FASTA
103 *Note* - Use a single genome fasta. Multiple FASTAs will not work.
104
105 **OUTPUT** -->
106 Protein sequences which passed the above filters are returned as the candidate USPs in three files: a protein FASTA file, a GFF3, and basic summary statistics text file.
107 .
108
109 ]]></help>
110 <citations>
111 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
112 <citation type="doi">https://dx.doi.org/10.1016/bs.aivir.2018.09.003</citation>
113 <citation type="bibtex">
114 @unpublished{galaxyTools,
115 author = {C. Ross},
116 title = {CPT Galaxy Tools},
117 year = {2020-},
118 note = {https://github.com/tamu-cpt/galaxy-tools/}
119 }
120 </citation>
121 </citations>
122 </tool>