Mercurial > repos > padge > clipkit
comparison clipkit.xml @ 2:e9cf321ee7be draft
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author | padge |
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date | Fri, 25 Mar 2022 17:33:41 +0000 |
parents | 49b058e85902 |
children | 770695339600 |
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1:535881934a1a | 2: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"> | 1 <tool id="clipkit" name="ClipKIT. Alignment trimming software for phylogenetics." version="0.1.0" python_template_version="3.5"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="1.3">clipkit</requirement> | 3 <requirement type="package" version="1.3">clipkit</requirement> |
4 </requirements> | 4 </requirements> |
5 <command detect_errors="exit_code"><![CDATA[ | 5 <command detect_errors="exit_code"><![CDATA[ |
6 clipkit $input1 -m ${mode_selector} -o $trimmed_output --log ${complement} | 6 clipkit $input1 -m ${mode_selector} -o $trimmed_output -of $out_format_selector --log ${complement} |
7 #if $gaps | 7 #if $gaps |
8 --gaps ${gaps} | 8 --gaps ${gaps} |
9 #end if; | 9 #end if; |
10 && | 10 && |
11 mv ${trimmed_output}.log ${log_output} | 11 mv ${trimmed_output}.log ${log_output} |
24 <option value="kpic-smart-gap">kpic-smart-gap</option> | 24 <option value="kpic-smart-gap">kpic-smart-gap</option> |
25 <option value="kpic-gappy">kpic-gappy</option> | 25 <option value="kpic-gappy">kpic-gappy</option> |
26 <option value="kpi">kpi</option> | 26 <option value="kpi">kpi</option> |
27 <option value="kpi-smart-gap">kpi-smart-gap</option> | 27 <option value="kpi-smart-gap">kpi-smart-gap</option> |
28 <option value="kpi-gappy">kpi-gappy</option> | 28 <option value="kpi-gappy">kpi-gappy</option> |
29 </param> | |
30 <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> | |
31 <option value="fasta">FASTA format</option> | |
32 <option value="clustal">CLUSTAL format</option> | |
33 <option value="maf">MAF format</option> | |
34 <option value="mauve">MAUVE format</option> | |
35 <option value="stockholm">STOCKHOLM format</option> | |
36 <option value="phylip">PHYLIP/PHYLIP4 format</option> | |
37 <option value="phylip_sequential">PHYLIP/PHYLIP4 sequential format</option> | |
38 <option value="phylip_relaxed">PHYLIP/PHYLIP4 relaxed format</option> | |
29 </param> | 39 </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"/> | 40 <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" /> | 41 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" /> |
32 </inputs> | 42 </inputs> |
33 <outputs> | 43 <outputs> |
64 <param name="complement" value="true" /> | 74 <param name="complement" value="true" /> |
65 <param name="gaps" value="0.9" /> | 75 <param name="gaps" value="0.9" /> |
66 <output name="trimmed_output" file="kpi.simple.fa.clipkit"/> | 76 <output name="trimmed_output" file="kpi.simple.fa.clipkit"/> |
67 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> | 77 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> |
68 </test> | 78 </test> |
79 <test> | |
80 <param name="input1" value="simple.fa"/> | |
81 <param name="mode_selector" value="kpi-gappy" /> | |
82 <param name="out_format_selector" value="phylip_relaxed" /> | |
83 <param name="gaps" value="0.7" /> | |
84 <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed"/> | |
85 <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/> | |
86 </test> | |
69 </tests> | 87 </tests> |
70 <help><![CDATA[ | 88 <help><![CDATA[ |
71 Modes | 89 Modes |
72 smart-gap: dynamic determination of gaps threshold | 90 smart-gap: dynamic determination of gaps threshold |
73 gappy: trim sites that are greater than the gaps threshold | 91 gappy: trim sites that are greater than the gaps threshold |
101 Complementary | 119 Complementary |
102 Creates an alignment file of only the trimmed sequences. | 120 Creates an alignment file of only the trimmed sequences. |
103 ]]></help> | 121 ]]></help> |
104 <citations> | 122 <citations> |
105 <citation type="bibtex"> | 123 <citation type="bibtex"> |
106 @misc{githubPhyKIT, | 124 @misc{githubClipKIT, |
107 author = {LastTODO, FirstTODO}, | 125 author = {LastTODO, FirstTODO}, |
108 year = {TODO}, | 126 year = {TODO}, |
109 title = {PhyKIT}, | 127 title = {ClipKIT}, |
110 publisher = {GitHub}, | 128 publisher = {GitHub}, |
111 journal = {GitHub repository}, | 129 journal = {GitHub repository}, |
112 url = {https://github.com/jlsteenwyk/clipkit}, | 130 url = {https://github.com/jlsteenwyk/clipkit}, |
113 }</citation> | 131 }</citation> |
114 </citations> | 132 </citations> |