Mercurial > repos > padge > clipkit
annotate clipkit.xml @ 4:770695339600 draft default tip
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
author | padge |
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date | Mon, 11 Apr 2022 13:08:12 +0000 |
parents | e9cf321ee7be |
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49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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1 <tool id="clipkit" name="ClipKIT. Alignment trimming software for phylogenetics." version="0.1.0" python_template_version="3.5"> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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2 <requirements> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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3 <requirement type="package" version="1.3">clipkit</requirement> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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4 </requirements> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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5 <command detect_errors="exit_code"><![CDATA[ |
2
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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6 clipkit $input1 -m ${mode_selector} -o $trimmed_output -of $out_format_selector --log ${complement} |
0
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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7 #if $gaps |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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8 --gaps ${gaps} |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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9 #end if; |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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10 && |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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11 mv ${trimmed_output}.log ${log_output} |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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12 #if $complement |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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13 && |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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14 mv ${trimmed_output}.complement ${complement_output} |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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15 #end if; |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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16 |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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17 ]]></command> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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18 <inputs> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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19 <param name="input1" type="data" format="fasta,clustal,maf,xmfa,phylip,stockholm" multiple="false" label="Alignment file" optional="false" /> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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20 <param name="mode_selector" type="select" label="Select trimming mode from the list"> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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21 <option value="smart-gap">smart-gap</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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22 <option value="gappy">gappy</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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23 <option value="kpic">kpic</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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24 <option value="kpic-smart-gap">kpic-smart-gap</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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25 <option value="kpic-gappy">kpic-gappy</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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26 <option value="kpi">kpi</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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27 <option value="kpi-smart-gap">kpi-smart-gap</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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28 <option value="kpi-gappy">kpi-gappy</option> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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29 </param> |
2
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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30 <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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31 <option value="fasta">FASTA format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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32 <option value="clustal">CLUSTAL format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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33 <option value="maf">MAF format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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34 <option value="mauve">MAUVE format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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35 <option value="stockholm">STOCKHOLM format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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36 <option value="phylip">PHYLIP/PHYLIP4 format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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37 <option value="phylip_sequential">PHYLIP/PHYLIP4 sequential format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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38 <option value="phylip_relaxed">PHYLIP/PHYLIP4 relaxed format</option> |
e9cf321ee7be
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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39 </param> |
0
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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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"/> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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41 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" /> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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42 </inputs> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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43 <outputs> |
4
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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44 <data name="trimmed_output" format="fasta" label="Trimmed alignment."> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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45 <!-- <filter>out_format_selector == 'fasta'</filter> --> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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46 <change_format> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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47 <when input="out_format_selector" value="fasta" format="fasta" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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48 <when input="out_format_selector" value="clustal" format="clustal" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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49 <when input="out_format_selector" value="maf" format="maf" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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50 <when input="out_format_selector" value="mauve" format="xmfa" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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51 <when input="out_format_selector" value="stockholm" format="stockholm" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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52 <when input="out_format_selector" value="phylip" format="phylip" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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53 <when input="out_format_selector" value="phylip_sequential" format="phylip" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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54 <when input="out_format_selector" value="phylip_relaxed" format="phylip" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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55 </change_format> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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56 </data> |
0
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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57 <data name="log_output" format="txt" label="Clipkit log."/> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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58 <data name="complement_output" format="fasta" label="Clipkit complement."> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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59 <filter>complement</filter> |
4
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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60 <change_format> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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61 <when input="out_format_selector" value="fasta" format="fasta" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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62 <when input="out_format_selector" value="clustal" format="clustal" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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63 <when input="out_format_selector" value="maf" format="maf" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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64 <when input="out_format_selector" value="mauve" format="xmfa" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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65 <when input="out_format_selector" value="stockholm" format="stockholm" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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66 <when input="out_format_selector" value="phylip" format="phylip" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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67 <when input="out_format_selector" value="phylip_sequential" format="phylip" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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68 <when input="out_format_selector" value="phylip_relaxed" format="phylip" /> |
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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69 </change_format> |
0
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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70 </data> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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71 </outputs> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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72 <tests> |
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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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73 <test> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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74 <param name="input1" value="simple.fa"/> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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75 <param name="mode_selector" value="smart-gap" /> |
4
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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76 <param name="out_format_selector" value="fasta" /> |
0
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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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77 <param name="gaps" value="0.9" /> |
4
770695339600
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
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78 <output name="trimmed_output" file="simple.fa.clipkit" ftype="fasta"/> |
0
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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79 <output name="log_output" file="simple.fa.clipkit.log"/> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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80 </test> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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81 <test> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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82 <param name="input1" value="simple.fa"/> |
49b058e85902
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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83 <param name="mode_selector" value="gappy" /> |
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84 <param name="out_format_selector" value="fasta" /> |
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85 <param name="gaps" value="0.2" /> |
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86 <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/> |
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87 </test> |
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88 <test> |
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89 <param name="input1" value="simple.fa"/> |
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90 <param name="mode_selector" value="gappy" /> |
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91 <param name="out_format_selector" value="fasta" /> |
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92 <param name="gaps" value="0.2" /> |
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93 <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/> |
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94 <output name="log_output" file="gappy.simple.fa.clipkit.log"/> |
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95 </test> |
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96 <test> |
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97 <param name="input1" value="simple.fa"/> |
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98 <param name="mode_selector" value="kpi" /> |
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99 <param name="complement" value="true" /> |
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100 <param name="out_format_selector" value="fasta" /> |
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101 <param name="gaps" value="0.9" /> |
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102 <output name="trimmed_output" file="kpi.simple.fa.clipkit" ftype="fasta"/> |
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103 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> |
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104 </test> |
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105 <test> |
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106 <param name="input1" value="simple.fa"/> |
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107 <param name="mode_selector" value="kpi-gappy" /> |
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108 <param name="out_format_selector" value="phylip_relaxed" /> |
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109 <param name="gaps" value="0.7" /> |
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110 <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed" ftype="phylip"/> |
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111 <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/> |
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112 </test> |
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113 </tests> |
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114 <help><![CDATA[ |
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115 Modes |
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116 smart-gap: dynamic determination of gaps threshold |
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117 gappy: trim sites that are greater than the gaps threshold |
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118 kpic: keeps parismony informative and constant sites |
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119 kpic-smart-gap: a combination of kpic- and smart-gap-based trimming |
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120 kpic-gappy: a combination of kpic- and gappy-based trimming |
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121 kpi: keep only parsimony informative sites |
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122 kpi-smart-gap: a combination of kpi- and smart-gap-based trimming |
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123 kpi-gappy: a combination of kpi- and gappy-based trimming |
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124 |
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125 Gaps |
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126 Positions with gappyness greater than threshold will be trimmed. |
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127 Must be between 0 and 1. (Default: 0.9). This argument is ignored |
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128 when using the kpi and kpic mdoes of trimming as well as an |
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129 iteration of trimming that uses smart-gap. |
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130 |
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131 Input and output file formats |
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132 Supported input and output files include: |
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133 fasta, clustal, maf, mauve, phylip, phylip-sequential, |
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134 phylip-relaxed, and stockholm |
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135 |
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136 Log |
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137 Creates a log file that summarizes the characteristics of each position. |
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138 The log file has four columns. |
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139 - Column 1 is the position in the alignment (starting at 1), |
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140 - Column 2 reports if the site was trimmed or kept (trim and keep, respectively), |
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141 - Column 3 reports if the site is a parsimony informative site or not (PI and nPI, respectively), or |
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142 a constant site or not (Const, nConst), or neither (nConst, nPI) |
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143 - Column 4 reports the gappyness of the the position (number of gaps / entries in alignment) |
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144 |
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145 Complementary |
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146 Creates an alignment file of only the trimmed sequences. |
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147 ]]></help> |
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148 <citations> |
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149 <citation type="bibtex"> |
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150 @misc{githubClipKIT, |
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151 author = {LastTODO, FirstTODO}, |
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152 year = {TODO}, |
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153 title = {ClipKIT}, |
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154 publisher = {GitHub}, |
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155 journal = {GitHub repository}, |
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156 url = {https://github.com/jlsteenwyk/clipkit}, |
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157 }</citation> |
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158 </citations> |
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159 </tool> |