Mercurial > repos > padge > clipkit
comparison clipkit.xml @ 4:770695339600 draft default tip
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
| author | padge |
|---|---|
| date | Mon, 11 Apr 2022 13:08:12 +0000 |
| parents | e9cf321ee7be |
| children |
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| 3:34f21474cdea | 4:770695339600 |
|---|---|
| 39 </param> | 39 </param> |
| 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"/> | 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"/> |
| 41 <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" /> |
| 42 </inputs> | 42 </inputs> |
| 43 <outputs> | 43 <outputs> |
| 44 <data name="trimmed_output" format="fasta" label="Trimmed alignment."/> | 44 <data name="trimmed_output" format="fasta" label="Trimmed alignment."> |
| 45 <!-- <filter>out_format_selector == 'fasta'</filter> --> | |
| 46 <change_format> | |
| 47 <when input="out_format_selector" value="fasta" format="fasta" /> | |
| 48 <when input="out_format_selector" value="clustal" format="clustal" /> | |
| 49 <when input="out_format_selector" value="maf" format="maf" /> | |
| 50 <when input="out_format_selector" value="mauve" format="xmfa" /> | |
| 51 <when input="out_format_selector" value="stockholm" format="stockholm" /> | |
| 52 <when input="out_format_selector" value="phylip" format="phylip" /> | |
| 53 <when input="out_format_selector" value="phylip_sequential" format="phylip" /> | |
| 54 <when input="out_format_selector" value="phylip_relaxed" format="phylip" /> | |
| 55 </change_format> | |
| 56 </data> | |
| 45 <data name="log_output" format="txt" label="Clipkit log."/> | 57 <data name="log_output" format="txt" label="Clipkit log."/> |
| 46 <data name="complement_output" format="fasta" label="Clipkit complement."> | 58 <data name="complement_output" format="fasta" label="Clipkit complement."> |
| 47 <filter>complement</filter> | 59 <filter>complement</filter> |
| 60 <change_format> | |
| 61 <when input="out_format_selector" value="fasta" format="fasta" /> | |
| 62 <when input="out_format_selector" value="clustal" format="clustal" /> | |
| 63 <when input="out_format_selector" value="maf" format="maf" /> | |
| 64 <when input="out_format_selector" value="mauve" format="xmfa" /> | |
| 65 <when input="out_format_selector" value="stockholm" format="stockholm" /> | |
| 66 <when input="out_format_selector" value="phylip" format="phylip" /> | |
| 67 <when input="out_format_selector" value="phylip_sequential" format="phylip" /> | |
| 68 <when input="out_format_selector" value="phylip_relaxed" format="phylip" /> | |
| 69 </change_format> | |
| 48 </data> | 70 </data> |
| 49 </outputs> | 71 </outputs> |
| 50 <tests> | 72 <tests> |
| 51 <test> | 73 <test> |
| 52 <param name="input1" value="simple.fa"/> | 74 <param name="input1" value="simple.fa"/> |
| 53 <param name="mode_selector" value="smart-gap" /> | 75 <param name="mode_selector" value="smart-gap" /> |
| 76 <param name="out_format_selector" value="fasta" /> | |
| 54 <param name="gaps" value="0.9" /> | 77 <param name="gaps" value="0.9" /> |
| 55 <output name="trimmed_output" file="simple.fa.clipkit"/> | 78 <output name="trimmed_output" file="simple.fa.clipkit" ftype="fasta"/> |
| 56 <output name="log_output" file="simple.fa.clipkit.log"/> | 79 <output name="log_output" file="simple.fa.clipkit.log"/> |
| 57 </test> | 80 </test> |
| 58 <test> | 81 <test> |
| 59 <param name="input1" value="simple.fa"/> | 82 <param name="input1" value="simple.fa"/> |
| 60 <param name="mode_selector" value="gappy" /> | 83 <param name="mode_selector" value="gappy" /> |
| 84 <param name="out_format_selector" value="fasta" /> | |
| 61 <param name="gaps" value="0.2" /> | 85 <param name="gaps" value="0.2" /> |
| 62 <output name="trimmed_output" file="gappy.simple.fa.clipkit"/> | 86 <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/> |
| 63 </test> | 87 </test> |
| 64 <test> | 88 <test> |
| 65 <param name="input1" value="simple.fa"/> | 89 <param name="input1" value="simple.fa"/> |
| 66 <param name="mode_selector" value="gappy" /> | 90 <param name="mode_selector" value="gappy" /> |
| 91 <param name="out_format_selector" value="fasta" /> | |
| 67 <param name="gaps" value="0.2" /> | 92 <param name="gaps" value="0.2" /> |
| 68 <output name="trimmed_output" file="gappy.simple.fa.clipkit"/> | 93 <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/> |
| 69 <output name="log_output" file="gappy.simple.fa.clipkit.log"/> | 94 <output name="log_output" file="gappy.simple.fa.clipkit.log"/> |
| 70 </test> | 95 </test> |
| 71 <test> | 96 <test> |
| 72 <param name="input1" value="simple.fa"/> | 97 <param name="input1" value="simple.fa"/> |
| 73 <param name="mode_selector" value="kpi" /> | 98 <param name="mode_selector" value="kpi" /> |
| 74 <param name="complement" value="true" /> | 99 <param name="complement" value="true" /> |
| 100 <param name="out_format_selector" value="fasta" /> | |
| 75 <param name="gaps" value="0.9" /> | 101 <param name="gaps" value="0.9" /> |
| 76 <output name="trimmed_output" file="kpi.simple.fa.clipkit"/> | 102 <output name="trimmed_output" file="kpi.simple.fa.clipkit" ftype="fasta"/> |
| 77 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> | 103 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> |
| 78 </test> | 104 </test> |
| 79 <test> | 105 <test> |
| 80 <param name="input1" value="simple.fa"/> | 106 <param name="input1" value="simple.fa"/> |
| 81 <param name="mode_selector" value="kpi-gappy" /> | 107 <param name="mode_selector" value="kpi-gappy" /> |
| 82 <param name="out_format_selector" value="phylip_relaxed" /> | 108 <param name="out_format_selector" value="phylip_relaxed" /> |
| 83 <param name="gaps" value="0.7" /> | 109 <param name="gaps" value="0.7" /> |
| 84 <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed"/> | 110 <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed" ftype="phylip"/> |
| 85 <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/> | 111 <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/> |
| 86 </test> | 112 </test> |
| 87 </tests> | 113 </tests> |
| 88 <help><![CDATA[ | 114 <help><![CDATA[ |
| 89 Modes | 115 Modes |