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comparison findSpanin.xml @ 3:fd70980a516b draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:42:01 +0000
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2:1a7fef71aee3 3:fd70980a516b
1 <tool id="edu.tamu.cpt2.spanin.findSpanin" name="Find Spanin" version="1.0">
2 <description>With the outputs from the ISP and OSP candidate tools, cull the list down to candidate pairs</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 '$__tool_directory__/findSpanin.py'
11 '$putative_isp_fasta_file'
12 '$putative_osp_fasta_file'
13 --max_isp_osp_distance '$max_isp_osp_distance'
14 --embedded_txt '$embedded_txt'
15 --overlap_txt '$overlap_txt'
16 --separate_txt '$separate_txt'
17 --summary_txt '$summary_txt'
18 ]]></command>
19 <inputs>
20 <param label="(putative) i-spanin FASTA file" name="putative_isp_fasta_file" type="data" format="fasta"/>
21 <param label="(putative) o-spanin FASTA file" name="putative_osp_fasta_file" type="data" format="fasta"/>
22 <param label="max distance from end of i-spanin to beginning of o-spanin (measured in AAs)" name="max_isp_osp_distance" type="integer" value="10"/>
23 </inputs>
24 <outputs>
25 <data format="txt" name="summary_txt" label="FindSpanin_summary.txt"/>
26 <data format="tabular" name="embedded_txt" label="embedded_results.txt"/>
27 <data format="tabular" name="overlap_txt" label="overlap_results.txt"/>
28 <data format="tabular" name="separate_txt" label="separate_results.txt"/>
29 </outputs>
30 <help><![CDATA[
31 **What it does**
32 Compares the protein FASTA files with candidate i-spanins and o-spanins from a genome and matches them into candidate pairs based on position in a strand-aware fashion.
33
34 **INPUT** --> Putative i-spanin and o-spanin protein multiFASTAs (generated from the ISP/OSP Candidate Tools).
35
36 **METHODOLOGY**
37 Does a pairwise comparison between candidate i-spanins and o-spanins based on their genomic location, and classifies them into the known bimolecular spanin genetic architectures. Classes are: embedded, overlapping, separated, or NOT a potential pair.
38
39 **OUTPUT** --> File with candidate pairs for each bimolecular spanin class and a basic summary statistics file.
40
41 ]]></help>
42 <expand macro="citations-2020"/>
43 </tool>