Mercurial > repos > chemteam > bio3d_pca_visualize

annotate visualize_pc.xml @ 0:d16c1aea2333 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
author chemteam
date Tue, 26 Feb 2019 08:26:54 -0500
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0
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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1 <tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@">
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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2 <description>Generate trajectories of principle components of motions</description>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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3 <macros>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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4 <import>macros.xml</import>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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5 </macros>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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6 <expand macro="requirements" />
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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7 <command detect_errors="exit_code">
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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8 <![CDATA[
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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9 Rscript '$__tool_directory__/visualize_pc.R'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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10 '$dcdin'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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11 '$pdbin'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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12 '$method'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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13 #if $pca.sele == 'calpha':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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14 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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15 "calpha"
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16 #end if
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17 #if $pca.sele == 'cbeta':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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18 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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19 '$pca.cbeta'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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20 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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21 #if $pca.sele == 'backbone':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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22 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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23 "backbone"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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24 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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25 #if $pca.sele == 'sidechain':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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26 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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27 "sidechain"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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28 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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29 #if $pca.sele == 'protein':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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30 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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31 "protein"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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32 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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33 #if $pca.sele == 'ligand':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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34 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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35 "ligand"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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36 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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37 #if $pca.sele == 'nucleic':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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38 "string"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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39 "nucleic"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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40 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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41 #if $pca.sele == 'elety':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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42 "elety"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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43 '$pca.elety'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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44 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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45 #if $pca.sele == 'resid':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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46 "resid"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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47 '$pca.resid'
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48 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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49 #if $pca.sele == 'segid':
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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50 "segid"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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51 '$pca.segid'
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52 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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53 '$pc_id'
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54 '$pdbout'
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55 2>&1
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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56 ]]></command>
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57 <inputs>
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58 <expand macro="analysis_inputs"/>
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59 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
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60 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
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61 <conditional name="pca">
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62 <param name="sele" type="select" label="Select domains">
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63 <option value="calpha">Calpha</option>
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64 <option value="cbeta">Cbeta</option>
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65 <option value="backbone">Backbone</option>
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66 <option value="sidechain">Sidechain</option>
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67 <option value="protein">Protein</option>
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68 <option value="ligand">Ligand</option>
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69 <option value="nucleic">Nucleic Acids</option>
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70 <option value="elety">Atom Names</option>
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71 <option value="resid">Resid</option>
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72 <option value="segid">Segid</option>
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73 </param>
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74 <when value="calpha"/>
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75 <when value="cbeta"/>
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76 <when value="backbone"/>
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77 <when value="sidechain"/>
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78 <when value="protein"/>
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79 <when value="ligand"/>
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80 <when value="nucleic"/>
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81 <when value="elety">
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82 <param name="elety" type="text" value="CA" label="Atom Name"/>
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83 </when>
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84 <when value="resid">
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85 <param name="resid" type="text" value="BGLC" label="Resid"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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86 </when>
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87 <when value="segid">
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88 <param name="segid" type="text" value="SUBS" label="Segid"/>
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89 </when>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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90 </conditional>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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91 <param name="pc_id" type="integer" value="1" label="Principle component id"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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92 </inputs>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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93 <outputs>
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94 <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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95 </outputs>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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96 <tests>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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97 <test>
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98 <expand macro="tests_inputs"/>
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99 <param name="method" value="false"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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100 <param name="sele" value="calpha"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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101 <param name="pc_id" value="1"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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102 <output name="pdbout" file="PCA_1.pdb" />
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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103 </test>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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104 </tests>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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105 <help><![CDATA[
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106 .. class:: infomark
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107
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108 **What it does**
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109
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110 This tool can generate small trajectories of a given principle component.
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111
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112 _____
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113
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114
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115 .. class:: infomark
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116
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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117 **Input**
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118
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119 - Input file in PDB format
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120 - Input file in dcd format
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121
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122 _____
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123
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124
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125 .. class:: infomark
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126
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127 **Output**
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128
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129 - A short trajectory (as PDB) of the given priciple component id.
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130
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131
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132 ]]></help>
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133 <expand macro="citations" />
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134 </tool>