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comparison virAnnot_otu.xml @ 0:e924ab4ab00a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
author iuc
date Wed, 21 Aug 2024 13:13:10 +0000
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1 <tool id="virannot_otu" name="virAnnot OTU" version="1.0.1+galaxy0" profile="21.05">
2 <description>create viral OTUs based on RPS and Blast annotations</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <required_files>
9 <include path="otu.py" />
10 <include path="seek_otu.R" />
11 <include path="rps2tree_html.py" />
12 </required_files>
13 <command detect_errors="aggressive"><![CDATA[
14
15 @HEADLESS@
16 #if $blast_files
17 #for $blast_file in $blast_files
18 ln -fs '$blast_file' '$blast_file.element_identifier' &&
19 #end for
20 #end if
21 #for $rps_file in $rps_files
22 ln -fs '$rps_file' '$rps_file.element_identifier' &&
23 #end for
24 #for $fasta_file in $fasta_files
25 ln -fs '$fasta_file' '$fasta_file.element_identifier' &&
26 #end for
27
28 python '$__tool_directory__/otu.py'
29 #if $blast_files
30 #for $blast_file in $blast_files
31 -b '$blast_file.element_identifier'
32 #end for
33 #end if
34 #for $rps_file in $rps_files
35 -r '$rps_file.element_identifier'
36 #end for
37 #for $fasta_file in $fasta_files
38 -f '$fasta_file.element_identifier'
39 #end for
40 -p '$percentage'
41 -vp '$viral_portion'
42 -mpl '$min_prot_length'
43 -tp '$__tool_directory__/'
44 -o otu_output
45
46 && zip -r out.zip otu_output
47
48 ]]></command>
49 <inputs>
50 <param type="data" name="blast_files" format="tabular" label="Blast results file with taxonomy" multiple="true" optional="true"
51 help="Give one file per sample. If a file is missing, give none." />
52 <param type="data" name="rps_files" format="tabular" label="RPS results file" multiple="true" />
53 <param type="data" name="fasta_files" format="fasta" label="Contigs file" multiple="true" />
54 <param type="integer" name="percentage" label="Similarity threshold percentage for OTUs cutoff" value="90" min="10" max="100" />
55 <param type="select" name="viral_portion" label="Minimun portion of viral sequences in RPS domain to be included">
56 <option value="0.1">0.1</option>
57 <option value="0.2">0.2</option>
58 <option value="0.3" selected="true">0.3</option>
59 <option value="0.4">0.4</option>
60 <option value="0.5">0.5</option>
61 </param>
62 <param type="select" name="min_prot_length" label="Minimum query protein length">
63 <option value="50">50</option>
64 <option value="80">80</option>
65 <option value="100" selected="true">100</option>
66 <option value="150">150</option>
67 <option value="200">200</option>
68 </param>
69 </inputs>
70 <outputs>
71 <data format="xlsx" name="otu_table" label="${tool.name} on ${on_string}: otu_stats" from_work_dir="otu_output/otu_stats.xlsx" />
72 <data format="zip" name="archive_output" label="${tool.name} on ${on_string}: zip of the complete output" from_work_dir="out.zip" />
73 </outputs>
74 <tests>
75 <test>
76 <param name="blast_files" value="otu_s1_tblastx.tab,otu_s2_tblastx.tab"/>
77 <param name="rps_files" value="otu_s1_rps.tab,otu_s2_rps.tab"/>
78 <param name="fasta_files" value="otu_s1.fa,otu_s2.fa"/>
79 <param name="percentage" value="90"/>
80 <param name="viral_portion" value="0.3"/>
81 <param name="min_prot_length" value="100"/>
82 <!-- check created zip -->
83 <output name="archive_output">
84 <assert_contents>
85 <has_archive_member path=".*\/index.html" />
86 <has_archive_member path=".*\/pfam00680_RdRP_1/seq_aligned.final_tree.fa" />
87 </assert_contents>
88 </output>
89 </test>
90 </tests>
91 <help><![CDATA[
92
93 This module takes as input rps file from rps2tsv, blast file from blastxml_to_tabular [optional] and fasta contig file [optional].
94
95 If no blast file is given, OTUs will not have an associated annotation i.e the OTUs will be set as unknown.
96 Files are processed in alphabetical order. Make sure that the files (blast, rps and contig) for a sample are named in the same way,
97 otherwise they will be disassociated.
98
99 The standard similarity threshold is 90% [default value] which is a proxy to viral species compared with the ICTV classification.
100
101 ]]></help>
102 <expand macro="citations" />
103 </tool>