Mercurial > repos > chemteam > mdanalysis_cosine_analysis

annotate pca_cosine.xml @ 0:ead44fe2be57 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:43:29 -0400
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ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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1 <tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@">
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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2 <description>Measure the cosine content of the PCA projection</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/pca_cosine.py'
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10 --idcd '$dcdin'
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11 --ipdb '$pdbin'
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12 --icomponents '$components'
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13 --iindex '$index'
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14 --output '$output'
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15 --cosout '$cosout'
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16 2>&1
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17 ]]></command>
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18 <inputs>
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19 <expand macro="analysis_inputs"/>
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20 <param name="components" type="integer" value="3" label="Number of components"/>
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21 <param name="index" type="integer" value="0" label="The index of the PCA component projection to be analyzed"/>
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="output" label="PCA Analysis raw data"/>
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25 <data format="txt" name="cosout" label="Cosine content of the PCA projection"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <expand macro="tests_inputs"/>
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30 <param name="components" value="3"/>
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31 <param name="index" value="0"/>
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32 <output name="cosout">
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33 <assert_contents>
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34 <has_text text="0.5832533" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 .. class:: infomark
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41
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42 **What it does**
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43
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44 The cosine content of the principal components is a good indicator for determine good or bad sampling and can be use to determine the convergence of the MD simulation.
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45 This tool can calculate the cosine content of a user define PCA projection.
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46 This tool use zero based indexes (0 is PC1).
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47
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48 _____
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49
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50
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51 .. class:: infomark
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52
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53 **Input**
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54
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55 - Trajectory file (DCD).
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56 - PDB file.
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57
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58 _____
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59
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60
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61 .. class:: infomark
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62
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63 **Output**
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64
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65 - The cosine content value.
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66 - Tab-separated file of raw data of first three principle component.
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67
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68 ]]></help>
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69 <expand macro="citations">
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70 <citation type="doi">10.1103/PhysRevE.65.031910</citation>
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71 </expand>
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72 </tool>