Mercurial > repos > padge > clipkit
comparison clipkit.xml @ 0:49b058e85902 draft
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author | padge |
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date | Fri, 25 Mar 2022 13:04:31 +0000 |
parents | |
children | e9cf321ee7be |
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1 <tool id="clipkit" name="ClipKIT. Alignment trimming software for phylogenetics." version="0.1.0" python_template_version="3.5"> | |
2 <requirements> | |
3 <requirement type="package" version="1.3">clipkit</requirement> | |
4 </requirements> | |
5 <command detect_errors="exit_code"><![CDATA[ | |
6 clipkit $input1 -m ${mode_selector} -o $trimmed_output --log ${complement} | |
7 #if $gaps | |
8 --gaps ${gaps} | |
9 #end if; | |
10 && | |
11 mv ${trimmed_output}.log ${log_output} | |
12 #if $complement | |
13 && | |
14 mv ${trimmed_output}.complement ${complement_output} | |
15 #end if; | |
16 | |
17 ]]></command> | |
18 <inputs> | |
19 <param name="input1" type="data" format="fasta,clustal,maf,xmfa,phylip,stockholm" multiple="false" label="Alignment file" optional="false" /> | |
20 <param name="mode_selector" type="select" label="Select trimming mode from the list"> | |
21 <option value="smart-gap">smart-gap</option> | |
22 <option value="gappy">gappy</option> | |
23 <option value="kpic">kpic</option> | |
24 <option value="kpic-smart-gap">kpic-smart-gap</option> | |
25 <option value="kpic-gappy">kpic-gappy</option> | |
26 <option value="kpi">kpi</option> | |
27 <option value="kpi-smart-gap">kpi-smart-gap</option> | |
28 <option value="kpi-gappy">kpi-gappy</option> | |
29 </param> | |
30 <param name="gaps" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gappyness" help="Specify gappyness threshold (between 0 and 1). Default: 0.9" multiple="false"/> | |
31 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" /> | |
32 </inputs> | |
33 <outputs> | |
34 <data name="trimmed_output" format="fasta" label="Trimmed alignment."/> | |
35 <data name="log_output" format="txt" label="Clipkit log."/> | |
36 <data name="complement_output" format="fasta" label="Clipkit complement."> | |
37 <filter>complement</filter> | |
38 </data> | |
39 </outputs> | |
40 <tests> | |
41 <test> | |
42 <param name="input1" value="simple.fa"/> | |
43 <param name="mode_selector" value="smart-gap" /> | |
44 <param name="gaps" value="0.9" /> | |
45 <output name="trimmed_output" file="simple.fa.clipkit"/> | |
46 <output name="log_output" file="simple.fa.clipkit.log"/> | |
47 </test> | |
48 <test> | |
49 <param name="input1" value="simple.fa"/> | |
50 <param name="mode_selector" value="gappy" /> | |
51 <param name="gaps" value="0.2" /> | |
52 <output name="trimmed_output" file="gappy.simple.fa.clipkit"/> | |
53 </test> | |
54 <test> | |
55 <param name="input1" value="simple.fa"/> | |
56 <param name="mode_selector" value="gappy" /> | |
57 <param name="gaps" value="0.2" /> | |
58 <output name="trimmed_output" file="gappy.simple.fa.clipkit"/> | |
59 <output name="log_output" file="gappy.simple.fa.clipkit.log"/> | |
60 </test> | |
61 <test> | |
62 <param name="input1" value="simple.fa"/> | |
63 <param name="mode_selector" value="kpi" /> | |
64 <param name="complement" value="true" /> | |
65 <param name="gaps" value="0.9" /> | |
66 <output name="trimmed_output" file="kpi.simple.fa.clipkit"/> | |
67 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> | |
68 </test> | |
69 </tests> | |
70 <help><![CDATA[ | |
71 Modes | |
72 smart-gap: dynamic determination of gaps threshold | |
73 gappy: trim sites that are greater than the gaps threshold | |
74 kpic: keeps parismony informative and constant sites | |
75 kpic-smart-gap: a combination of kpic- and smart-gap-based trimming | |
76 kpic-gappy: a combination of kpic- and gappy-based trimming | |
77 kpi: keep only parsimony informative sites | |
78 kpi-smart-gap: a combination of kpi- and smart-gap-based trimming | |
79 kpi-gappy: a combination of kpi- and gappy-based trimming | |
80 | |
81 Gaps | |
82 Positions with gappyness greater than threshold will be trimmed. | |
83 Must be between 0 and 1. (Default: 0.9). This argument is ignored | |
84 when using the kpi and kpic mdoes of trimming as well as an | |
85 iteration of trimming that uses smart-gap. | |
86 | |
87 Input and output file formats | |
88 Supported input and output files include: | |
89 fasta, clustal, maf, mauve, phylip, phylip-sequential, | |
90 phylip-relaxed, and stockholm | |
91 | |
92 Log | |
93 Creates a log file that summarizes the characteristics of each position. | |
94 The log file has four columns. | |
95 - Column 1 is the position in the alignment (starting at 1), | |
96 - Column 2 reports if the site was trimmed or kept (trim and keep, respectively), | |
97 - Column 3 reports if the site is a parsimony informative site or not (PI and nPI, respectively), or | |
98 a constant site or not (Const, nConst), or neither (nConst, nPI) | |
99 - Column 4 reports the gappyness of the the position (number of gaps / entries in alignment) | |
100 | |
101 Complementary | |
102 Creates an alignment file of only the trimmed sequences. | |
103 ]]></help> | |
104 <citations> | |
105 <citation type="bibtex"> | |
106 @misc{githubPhyKIT, | |
107 author = {LastTODO, FirstTODO}, | |
108 year = {TODO}, | |
109 title = {PhyKIT}, | |
110 publisher = {GitHub}, | |
111 journal = {GitHub repository}, | |
112 url = {https://github.com/jlsteenwyk/clipkit}, | |
113 }</citation> | |
114 </citations> | |
115 </tool> |