Mercurial > repos > chemteam > bio3d_pca_visualize

annotate visualize_pc.xml @ 3:eebc574b0923 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:30:37 -0400
parents d16c1aea2333
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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@">
3
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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2 <description>- generate trajectories of principal components of atomic motion</description>
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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"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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16 #end if
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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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'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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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'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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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 '$pc_id'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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54 '$pdbout'
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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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>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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57 <inputs>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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58 <expand macro="analysis_inputs"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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59 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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60 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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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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eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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63 <option value="calpha">C-alpha</option>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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64 <option value="cbeta">C-beta</option>
0
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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>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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68 <option value="ligand">Ligand</option>
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eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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69 <option value="nucleic">Nucleic acids</option>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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70 <option value="elety">Atom names</option>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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71 <option value="resid">Residue ID</option>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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72 <option value="segid">Segment ID</option>
0
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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73 </param>
3
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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74 <when value="calpha">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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75 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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76 <when value="cbeta">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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77 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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78 <when value="backbone">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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79 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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80 <when value="sidechain">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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81 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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82 <when value="protein">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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83 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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84 <when value="ligand">
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85 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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86 <when value="nucleic">
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87 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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88 <when value="elety">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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89 <param name="elety" type="text" value="CA" label="Atom name"/>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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90 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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91 <when value="resid">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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92 <param name="resid" type="text" value="BGLC" label="Residue ID"/>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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93 </when>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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94 <when value="segid">
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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95 <param name="segid" type="text" value="SUBS" label="Segment ID"/>
eebc574b0923 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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96 </when>
0
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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97 </conditional>
3
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98 <param name="pc_id" type="integer" value="1" label="Principal component ID"/>
0
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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99 </inputs>
3
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100
0
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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101 <outputs>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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102 <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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103 </outputs>
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 <test>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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106 <expand macro="tests_inputs"/>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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107 <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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108 <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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109 <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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110 <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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111 </test>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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112 </tests>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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113 <help><![CDATA[
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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114 .. class:: infomark
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115
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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116 **What it does**
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117
3
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118 This tool can generate small trajectories of a given principal component.
0
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119
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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120 _____
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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121
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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122
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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123 .. class:: infomark
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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124
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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125 **Input**
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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126
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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127 - Input file in PDB format
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128 - Input file in DCD format
0
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129
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130 _____
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131
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132
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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133 .. class:: infomark
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134
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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135 **Output**
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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136
3
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137 - A short trajectory (as PDB) of the given principal component ID.
0
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138
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139
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140 ]]></help>
d16c1aea2333 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
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141 <expand macro="citations" />
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142 </tool>