Mercurial > repos > chemteam > bio3d_pca

annotate pca.xml @ 0:f56fb2762abb draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
author chemteam
date Mon, 08 Oct 2018 12:49:36 -0400
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children 54dd1596e04e
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0
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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1 <tool id="bio3d_pca" name="PCA" version="@VERSION@">
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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2 <description>Principle component analysis using Bio3D</description>
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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3 <macros>
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4 <import>macros.xml</import>
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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5 </macros>
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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9 Rscript '$__tool_directory__/pca.R'
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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10 '$dcdin'
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11 '$pdbin'
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12 '$method'
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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13 #if $pca.sele == 'calpha':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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14 "string"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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15 "calpha"
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16 #end if
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17 #if $pca.sele == 'cbeta':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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18 "string"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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19 '$pca.cbeta'
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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20 #end if
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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21 #if $pca.sele == 'backbone':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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22 "string"
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23 "backbone"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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24 #end if
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25 #if $pca.sele == 'sidechain':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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26 "string"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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27 "sidechain"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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28 #end if
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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29 #if $pca.sele == 'protein':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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30 "string"
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31 "protein"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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32 #end if
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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33 #if $pca.sele == 'ligand':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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34 "string"
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35 "ligand"
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36 #end if
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37 #if $pca.sele == 'nucleic':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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38 "string"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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39 "nucleic"
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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40 #end if
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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41 #if $pca.sele == 'elety':
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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42 "elety"
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43 '$pca.elety'
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44 #end if
f56fb2762abb planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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45 #if $pca.sele == 'resid':
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46 "resid"
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47 '$pca.resid'
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48 #end if
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49 #if $pca.sele == 'segid':
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50 "segid"
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51 '$pca.segid'
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52 #end if
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53 '$output'
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54 '$pca_plot'
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55 '$pca_cluster'
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56 '$pc1_rmsf'
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57 2>&1
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58 ]]></command>
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59 <inputs>
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60 <expand macro="analysis_inputs"/>
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61 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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62 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
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63 <conditional name="pca">
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64 <param name="sele" type="select" label="Select domains">
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65 <option value="calpha">Calpha</option>
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66 <option value="cbeta">Cbeta</option>
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67 <option value="backbone">Backbone</option>
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68 <option value="sidechain">Sidechain</option>
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69 <option value="protein">Protein</option>
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70 <option value="ligand">Ligand</option>
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71 <option value="nucleic">Nucleic Acids</option>
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72 <option value="elety">Atom Names</option>
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73 <option value="resid">Resid</option>
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74 <option value="segid">Segid</option>
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75 </param>
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76 <when value="calpha">
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77 </when>
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78 <when value="cbeta">
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79 </when>
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80 <when value="backbone">
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81 </when>
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82 <when value="sidechain">
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83 </when>
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84 <when value="protein">
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85 </when>
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86 <when value="ligand">
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87 </when>
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88 <when value="nucleic">
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89 </when>
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90 <when value="elety">
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91 <param name="elety" type="text" value="CA" label="Atom Name"/>
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92 </when>
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93 <when value="resid">
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94 <param name="resid" type="text" value="BGLC" label="Resid"/>
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95 </when>
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96 <when value="segid">
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97 <param name="segid" type="text" value="SUBS" label="Segid"/>
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98 </when>
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99 </conditional>
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100 </inputs>
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101 <outputs>
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102 <data format="tabular" name="output" label="PCA raw data"/>
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103 <data format="png" name="pca_plot" label="PCA plot"/>
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104 <data format="png" name="pca_cluster" label="PCA Cluster Plot"/>
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105 <data format="png" name="pc1_rmsf" label="PC1 on RMSF"/>
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106 </outputs>
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107 <tests>
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108 <test>
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109 <expand macro="tests_inputs"/>
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110 <param name="method" value="false"/>
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111 <param name="sele" value="calpha"/>
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112 <output name="output">
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113 <assert_contents>
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114 <has_n_columns n="4" />
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115 </assert_contents>
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116 </output>
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120 .. class:: infomark
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121
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122 **What it does**
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123
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124 PCA can be used to determine the relationship between statistically meaningful conformations (major global motions)
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125 sampled during the trajectory.
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126
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127 _____
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128
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129
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130 .. class:: infomark
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131
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132 **Input**
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133
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134 - Input file in PDB format
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135 - Input file in dcd format
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136
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137 _____
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138
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139
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140 .. class:: infomark
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141
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142 **Output**
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143
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144 - Image (as PNG) of the pca plot
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145 - Image (as PNG) of the pca clusterd plot
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146 - Image (as PNG) of the PC1 plotted on RMSF
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147 - Tab-separated file of raw data
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148
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149 ]]></help>
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150 <expand macro="citations" />
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151 </tool>