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comparison PSM_Recombine.xml @ 1:97ef96676b48 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:26 +0000
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0:b18e8268bf4e 1:97ef96676b48
1 <tool id="edu.tamu.cpt.external.psm_recombine" name="PSM Prep and Table Generator:" version="21.0.0">
2 <description>: generates a raw PSM file for plotting and a tabular summary</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
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 <requirement type="package" version="3.7">python</requirement>
14 <requirement type="package" version="1.74">biopython</requirement>
15 </requirements>
16 <command detect_errors="aggressive"><![CDATA[
17 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_0_prep.pl'
18 --galaxy
19 --outfile_supporting '$__new_file_path__'
20 #for $item in $repeat_file:
21 --file "${item.file}"
22 #end for
23
24 --cpt_psm_object "${cpt_psm_object}"
25
26 --cpt_psm_object_files_path "${cpt_psm_object.files_path}"
27
28 --cpt_psm_object_format "TXT"
29
30 --cpt_psm_object_id "${cpt_psm_object.id}"
31
32 &&
33
34 mkdir tmp_001
35 &&
36 mkdir tmp_002
37
38 &&
39
40 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_2_gentable.pl'
41 --galaxy
42 --outfile_supporting '$__new_file_path__'
43 --file "${cpt_psm_object}"
44
45 #if $evalue and $evalue is not "None":
46 --evalue "${evalue}"
47 #end if
48
49 #if $dice and $dice is not "None":
50 --dice "${dice}"
51 #end if
52
53 #if $mismatch and $mismatch is not "None":
54 --mismatch "${mismatch}"
55 #end if
56
57 #if $gap_penalty and $gap_penalty is not "None":
58 --gap_penalty "${gap_penalty}"
59 #end if
60
61 #if $match and $match is not "None":
62 --match "${match}"
63 #end if
64
65 --diff_table "./tmpDiff.tsv"
66 --diff_table_files_path "./tmp_001"
67 --diff_table_format TSV_U
68 --diff_table_id "000001"
69
70 --blastclust "./tmpClust.tsv"
71 --blastclust_files_path "./tmp_002"
72 --blastclust_format TSV_U
73 --blastclust_id "000002"
74
75 &&
76
77 '$__tool_directory__/PSM_Recombine.py'
78 ./tmpDiff.tsv
79 #for $item in $repeat_file:
80 "${item.file}"
81 #end for
82 > "${tableOut}"
83 ]]>
84 </command>
85 <inputs>
86 <repeat name="repeat_file" title="Genbank file(s) used to generate PSM">
87 <param name="file" optional="False" label="Gbk file" type="data" format="genbank"/>
88 </repeat>
89 <param value="0.0001" name="evalue" help="Evalue cutoff" optional="True" label="evalue" type="float"/>
90 <param value="50" name="dice" help="Dice cutoff" optional="True" label="dice" type="float"/>
91 <param value="-1" name="mismatch" help="Mismatch Score" optional="True" label="mismatch" type="float"/>
92 <param value="0.0" name="gap_penalty" help="Gap Penalty" optional="True" label="gap_penalty" type="float"/>
93 <param value="5" name="match" help="Match Score" optional="True" label="match" type="float"/>
94 </inputs>
95 <outputs>
96 <data format="tabular" name="tableOut" label="PSM Tabular Results"/>
97 <data name="cpt_psm_object" label="Raw PSM Binary output" format="TXT"/>
98 </outputs>
99 <help><![CDATA[
100 **What it does**
101
102 This tool takes in 2 or more GenBank files, blasts, and prepares data
103 structures for use in the companion tool, PSM Plotter, as well as a
104 tabular file read-out of the results. Select as many (multi)-gbk files
105 as you *might* want to plot. Once this tool is done, you can select
106 any subset of those to plot then.
107
108 IMPORTANT PARAMETERS
109 --------------------
110
111 - ``mismatch``, ``gap_penalty``, ``match``
112
113 These parameters control the Needleman-Wunsch Multiple Sequence
114 Alignment library's scoring scheme. Mismatch scores are generally
115 negative and discourage unrelated proteins from being plotted in a
116 line together. Match scores encourage related proteins to line up.
117 Gap penalty is set at zero as we generally prefer gaps to mismatches
118 in this tool; phage genomes are small and gaps are "cheap" to use,
119 whereas mismatches can sometimes give an incorrect impression of
120 relatedness. That said, how your plots look is completely up to you
121 and we encourage experimentation!
122 ]]></help>
123 <expand macro="citations-2020"/>
124 </tool>