annotate clipkit.xml @ 3:34f21474cdea draft

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author padge
date Fri, 25 Mar 2022 17:35:03 +0000
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children 770695339600
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1 <tool id="clipkit" name="ClipKIT. Alignment trimming software for phylogenetics." version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="1.3">clipkit</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 clipkit $input1 -m ${mode_selector} -o $trimmed_output -of $out_format_selector --log ${complement}
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7 #if $gaps
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8 --gaps ${gaps}
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9 #end if;
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10 &&
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11 mv ${trimmed_output}.log ${log_output}
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12 #if $complement
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13 &&
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14 mv ${trimmed_output}.complement ${complement_output}
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15 #end if;
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16
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17 ]]></command>
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18 <inputs>
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19 <param name="input1" type="data" format="fasta,clustal,maf,xmfa,phylip,stockholm" multiple="false" label="Alignment file" optional="false" />
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20 <param name="mode_selector" type="select" label="Select trimming mode from the list">
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21 <option value="smart-gap">smart-gap</option>
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22 <option value="gappy">gappy</option>
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23 <option value="kpic">kpic</option>
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24 <option value="kpic-smart-gap">kpic-smart-gap</option>
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25 <option value="kpic-gappy">kpic-gappy</option>
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26 <option value="kpi">kpi</option>
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27 <option value="kpi-smart-gap">kpi-smart-gap</option>
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28 <option value="kpi-gappy">kpi-gappy</option>
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29 </param>
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30 <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
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31 <option value="fasta">FASTA format</option>
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32 <option value="clustal">CLUSTAL format</option>
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33 <option value="maf">MAF format</option>
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34 <option value="mauve">MAUVE format</option>
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35 <option value="stockholm">STOCKHOLM format</option>
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36 <option value="phylip">PHYLIP/PHYLIP4 format</option>
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37 <option value="phylip_sequential">PHYLIP/PHYLIP4 sequential format</option>
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38 <option value="phylip_relaxed">PHYLIP/PHYLIP4 relaxed format</option>
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39 </param>
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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"/>
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41 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" />
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42 </inputs>
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43 <outputs>
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44 <data name="trimmed_output" format="fasta" label="Trimmed alignment."/>
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45 <data name="log_output" format="txt" label="Clipkit log."/>
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46 <data name="complement_output" format="fasta" label="Clipkit complement.">
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47 <filter>complement</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input1" value="simple.fa"/>
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53 <param name="mode_selector" value="smart-gap" />
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54 <param name="gaps" value="0.9" />
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55 <output name="trimmed_output" file="simple.fa.clipkit"/>
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56 <output name="log_output" file="simple.fa.clipkit.log"/>
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57 </test>
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58 <test>
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59 <param name="input1" value="simple.fa"/>
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60 <param name="mode_selector" value="gappy" />
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61 <param name="gaps" value="0.2" />
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62 <output name="trimmed_output" file="gappy.simple.fa.clipkit"/>
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63 </test>
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64 <test>
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65 <param name="input1" value="simple.fa"/>
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66 <param name="mode_selector" value="gappy" />
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67 <param name="gaps" value="0.2" />
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68 <output name="trimmed_output" file="gappy.simple.fa.clipkit"/>
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69 <output name="log_output" file="gappy.simple.fa.clipkit.log"/>
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70 </test>
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71 <test>
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72 <param name="input1" value="simple.fa"/>
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73 <param name="mode_selector" value="kpi" />
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74 <param name="complement" value="true" />
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75 <param name="gaps" value="0.9" />
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76 <output name="trimmed_output" file="kpi.simple.fa.clipkit"/>
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77 <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/>
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78 </test>
2
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79 <test>
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80 <param name="input1" value="simple.fa"/>
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81 <param name="mode_selector" value="kpi-gappy" />
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82 <param name="out_format_selector" value="phylip_relaxed" />
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83 <param name="gaps" value="0.7" />
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84 <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed"/>
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85 <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/>
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86 </test>
0
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87 </tests>
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88 <help><![CDATA[
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89 Modes
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90 smart-gap: dynamic determination of gaps threshold
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91 gappy: trim sites that are greater than the gaps threshold
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92 kpic: keeps parismony informative and constant sites
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93 kpic-smart-gap: a combination of kpic- and smart-gap-based trimming
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94 kpic-gappy: a combination of kpic- and gappy-based trimming
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95 kpi: keep only parsimony informative sites
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96 kpi-smart-gap: a combination of kpi- and smart-gap-based trimming
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97 kpi-gappy: a combination of kpi- and gappy-based trimming
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98
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99 Gaps
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100 Positions with gappyness greater than threshold will be trimmed.
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101 Must be between 0 and 1. (Default: 0.9). This argument is ignored
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102 when using the kpi and kpic mdoes of trimming as well as an
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103 iteration of trimming that uses smart-gap.
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104
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105 Input and output file formats
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106 Supported input and output files include:
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107 fasta, clustal, maf, mauve, phylip, phylip-sequential,
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108 phylip-relaxed, and stockholm
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109
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110 Log
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111 Creates a log file that summarizes the characteristics of each position.
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112 The log file has four columns.
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113 - Column 1 is the position in the alignment (starting at 1),
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114 - Column 2 reports if the site was trimmed or kept (trim and keep, respectively),
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115 - Column 3 reports if the site is a parsimony informative site or not (PI and nPI, respectively), or
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116 a constant site or not (Const, nConst), or neither (nConst, nPI)
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117 - Column 4 reports the gappyness of the the position (number of gaps / entries in alignment)
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118
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119 Complementary
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120 Creates an alignment file of only the trimmed sequences.
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121 ]]></help>
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122 <citations>
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123 <citation type="bibtex">
2
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124 @misc{githubClipKIT,
0
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125 author = {LastTODO, FirstTODO},
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126 year = {TODO},
2
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127 title = {ClipKIT},
0
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128 publisher = {GitHub},
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129 journal = {GitHub repository},
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130 url = {https://github.com/jlsteenwyk/clipkit},
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131 }</citation>
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132 </citations>
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133 </tool>