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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 <tool id="PSM.Comp" name="PSM Comparison Table" version="1.94">
2 <description>aligns and lists data from PSM Prep</description>
3 <version_command>perl cpt_psm_2_gentable.pl --version</version_command>
4 <stdio>
5 <exit_code range="1:" level="fatal"/>
6 </stdio>
7 <requirements>
8 <requirement type="package" version="5.22.1">perl</requirement>
9 <requirement type="package">perl-bioperl</requirement>
10 <requirement type="package">perl-moose</requirement>
11 <requirement type="package">perl-ipc-run</requirement>
12 <requirement type="package">perl-getopt-long-descriptive</requirement>
13 </requirements>
14 <command detect_errors="aggressive"><![CDATA[
15 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_2_gentable.pl'
16 --galaxy
17 --outfile_supporting '$__new_file_path__'
18 --file "${file}"
19
20 #if $evalue and $evalue is not "None":
21 --evalue "${evalue}"
22 #end if
23
24 #if $dice and $dice is not "None":
25 --dice "${dice}"
26 #end if
27
28 #if $mismatch and $mismatch is not "None":
29 --mismatch "${mismatch}"
30 #end if
31
32 #if $gap_penalty and $gap_penalty is not "None":
33 --gap_penalty "${gap_penalty}"
34 #end if
35
36 #if $match and $match is not "None":
37 --match "${match}"
38 #end if
39
40 --diff_table "${diff_table}"
41 --diff_table_files_path "${diff_table.files_path}"
42 --diff_table_format TSV_U
43 --diff_table_id "${diff_table.id}"
44
45 --blastclust "${blastclust}"
46 --blastclust_files_path "${blastclust.files_path}"
47 --blastclust_format TSV_U
48 --blastclust_id "${blastclust.id}"
49
50 ]]></command>
51 <inputs>
52 <param name="file" help="PSM2 Data File" optional="False" label="file" type="data"/>
53 <param value="0.0001" name="evalue" help="Evalue cutoff" optional="True" label="evalue" type="float"/>
54 <param value="50" name="dice" help="Dice cutoff" optional="True" label="dice" type="float"/>
55 <param value="-1" name="mismatch" help="Mismatch Score" optional="True" label="mismatch" type="float"/>
56 <param value="0.0" name="gap_penalty" help="Gap Penalty" optional="True" label="gap_penalty" type="float"/>
57 <param value="5" name="match" help="Match Score" optional="True" label="match" type="float"/>
58 </inputs>
59 <outputs>
60 <data name="diff_table" format="tabular">
61 </data>
62 <data name="blastclust" format="tabular">
63 </data>
64 </outputs>
65 <help>DESCRIPTION
66 ===========
67
68 Following the execution of the PSM Prep tool, this tool simply aligns
69 the genomes and generates a table comparison the positions of all
70 proteins. It can be very useful to figure out which genes are missing in
71 which genomes.
72
73 IMPORTANT PARAMETERS
74 --------------------
75
76 - ``mismatch``, ``gap_penalty``, ``match``
77
78 These parameters control the Needleman-Wunsch Multiple Sequence
79 Alignment library's scoring scheme. Mismatch scores are generally
80 negative and discourage unrelated proteins from being plotted in a
81 line together. Match scores encourage related proteins to line up.
82 Gap penalty is set at zero as we generally prefer gaps to mismatches
83 in this tool; phage genomes are small and gaps are "cheap" to use,
84 whereas mismatches can sometimes give an incorrect impression of
85 relatedness. That said, how your plots look is completely up to you
86 and we encourage experimentation!
87
88
89 </help>
90 <tests/>
91 </tool>