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annotate fastpca.xml @ 0:7dbe8bd02431 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
author chemteam
date Thu, 30 Jan 2020 12:58:19 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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1 <tool id="fastpca" name="fastpca" version="@VERSION@">
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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2 <description>- dimensionality reduction of MD simulations</description>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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3 <macros>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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4 <token name="@VERSION@">0.9.1</token>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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5 </macros>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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6 <requirements>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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7 <requirement type="package" version="@VERSION@">fastpca</requirement>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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8 </requirements>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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9 <command detect_errors="exit_code"><![CDATA[
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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10 fastpca
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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11 -f '$input'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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12 -p '$output_proj'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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13 #if str($inputs.cov) == 'None':
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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14 -c '$output_cov'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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15 #elif str($inputs.vec) == 'None':
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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16 -C '$inputs.cov'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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17 #end if
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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18 #if str($inputs.vec) == 'None':
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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19 -v $output_vec
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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20 #else:
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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21 -V '$inputs.vec'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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22 #end if
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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23 #if str($inputs.stats) == 'None':
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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24 -s '$output_stats'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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25 #else:
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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26 -S '$inputs.stats'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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27 #end if
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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28 -l '$output_val'
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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29 $norm
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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30 $periodic
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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31 $dynamic_shift
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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32 --verbose
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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33
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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34 ]]></command>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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35 <inputs>
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36 <param format="tabular,xtc" name="input" type="data" label="Input data" help="Either a whitespace-separated tabular file or GROMACS XTC file."/>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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37 <section name="inputs" title="Inputs" expanded="true" help="Use these (optional) inputs to project new data onto a previously computed principal space. If not set, the PCA will be computed from scratch and will not be comparable to previous runs." >
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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38 <param format="tabular" name="cov" type="data" label="Precomputed covariance/correlation matrix" optional="true"/>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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39 <param format="tabular" name="vec" type="data" label="Precomputed eigenvectors" optional="true"/>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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40 <param format="tabular" name="stats" type="data" label="Precomputed statistics (mean values, sigmas and boundary shifts)" optional="true"/>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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41 </section>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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42
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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43 <param name="norm" type="select" label="How to normalize input:" help="Generally, normalization using the covariance matrix is appropriate when the variable scales are similar, and the correlation matrix is used when variables are on different scales." >
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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44 <option value="">Covariance</option>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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45 <option value="-N">Correlation</option>
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46 </param>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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47 <param name="periodic" type="boolean" label="Compute covariance and PCA on a torus?" truevalue="-P" falsevalue="" value="false" help="Useful for computing PCA on periodic data - for example, dihedral angles."/>
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48 <param name="dynamic_shift" type="boolean" label="Use dynamic shifting for periodic projection correction" truevalue="-D" falsevalue="" value="false" help="Default is fale, i.e. simply shift to region of lowest density"/>
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49 </inputs>
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50 <outputs>
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51 <data name="output_proj" format="tabular"/>
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52 <data name="output_cov" format="tabular">
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53 <filter>inputs["cov"] == None</filter>
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54 </data>
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55 <data name="output_vec" format="tabular">
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56 <filter>inputs["vec"] == None</filter>
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57 </data>
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58 <data name="output_stats" format="tabular">
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59 <filter>inputs["stats"] == None</filter>
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60 </data>
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61 <data name="output_val" format="tabular"/>
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62 </outputs>
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63 <tests>
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64 <!-- fastpca -f contacts.dat -p proj.dat -c cov.dat -v vec.dat -s stats.dat -l val.dat -N -->
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65 <test>
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66 <param name="input" value="contacts.dat"/>
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67 <param name="norm" value="-N"/>
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68 <param name="periodic" value="false"/>
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69 <param name="dynamic_shift" value="false"/>
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70 <output name="output_proj" file="proj.dat"/>
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71 <output name="output_cov" file="cov.dat"/>
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72 <output name="output_vec" file="vec.dat"/>
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73 <output name="output_stats" file="stats.dat"/>
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74 <output name="output_val" file="val.dat"/>
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75 </test>
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76 <!-- fastpca -f contacts2.dat -p proj2.dat -C cov.dat -V vec.dat -S stats.dat -l val2.dat -N -->
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77 <test>
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78 <param name="input" value="contacts2.dat"/>
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79 <param name="cov" value="cov.dat"/>
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80 <param name="stats" value="stats.dat"/>
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81 <param name="norm" value="-N"/>
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82 <param name="periodic" value="false"/>
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83 <param name="dynamic_shift" value="false"/>
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84 <output name="output_proj" file="proj2.dat"/>
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85 <output name="output_val" file="val2.dat"/>
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86 </test>
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87 </tests>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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88 <help><![CDATA[
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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89 .. class:: infomark
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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90
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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91 **What it does**
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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92
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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93 Dimensionality reduction of molecular dynamics trajectories. Data can be input as
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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94 tabular or GROMACS XTC files. In addition, data can be projected into a previously
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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95 computed coordinate space by providing precomputed eigenvectors, statistics and
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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96 a correlation/covariance matrix.
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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97
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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98 Data can be normalized using the either the covariance or correlation matrix. Data
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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99 can also be calculated on a torus, which is useful for periodic data, such as protein
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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100 dihedral angles.
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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101
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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102 _____
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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103
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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104
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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105 .. class:: infomark
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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106
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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107 **Input**
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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108
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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109 - Tabular or XTC file
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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110 - If you want to project data into a previously calculated principal space, you can upload precomputed eigenvectors, statistics and correlation/covariance matrix.
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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111
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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112 _____
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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113
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114
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115 .. class:: infomark
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116
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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117 **Output**
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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118
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119 - Projected data (tabular file) with each column representing a principal component
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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120 - Eigenvectors, statistics and covariance/correlation matrix
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121
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122 ]]></help>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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123 <citations>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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124 <citation type="doi">10.1063/1.4998259</citation>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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125 </citations>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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126 </tool>
7dbe8bd02431 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588"
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127