Mercurial > repos > padge > clipkit

comparison clipkit.xml @ 4:770695339600 draft default tip

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"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
comparison
equal deleted inserted replaced
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