Mercurial > repos > chemteam > mdanalysis_cosine_analysis
comparison pca_cosine.xml @ 1:d18e7db42633 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:50:44 -0400 |
| parents | ebeb72aa39a8 |
| children | a842da7ef42b |
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| 0:ebeb72aa39a8 | 1:d18e7db42633 |
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| 1 <tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@"> | 1 <tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@"> |
| 2 <description>Measure the cosine content of the PCA projection</description> | 2 <description>- measure the cosine content of the PCA projection</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
| 8 <![CDATA[ | 8 <![CDATA[ |
| 9 python '$__tool_directory__/pca_cosine.py' | 9 python '$__tool_directory__/pca_cosine.py' |
| 10 --idcd '$dcdin' | 10 --itraj '$trajin' |
| 11 --ipdb '$pdbin' | 11 --istr '$strin' |
| 12 --itrajext '$trajin.ext' | |
| 13 --istrext '$strin.ext' | |
| 12 --icomponents '$components' | 14 --icomponents '$components' |
| 13 --iindex '$index' | 15 --iindex '$index' |
| 14 --output '$output' | 16 --output '$output' |
| 15 --cosout '$cosout' | 17 --cosout '$cosout' |
| 16 2>&1 | 18 2>&1 |
| 33 <assert_contents> | 35 <assert_contents> |
| 34 <has_text text="0.5832533" /> | 36 <has_text text="0.5832533" /> |
| 35 </assert_contents> | 37 </assert_contents> |
| 36 </output> | 38 </output> |
| 37 </test> | 39 </test> |
| 40 <test> | |
| 41 <expand macro="tests_inputs_gmx"/> | |
| 42 <param name="components" value="3"/> | |
| 43 <param name="index" value="0"/> | |
| 44 <output name="cosout"> | |
| 45 <assert_contents> | |
| 46 <has_text text="0.583" /> | |
| 47 </assert_contents> | |
| 48 </output> | |
| 49 </test> | |
| 38 </tests> | 50 </tests> |
| 39 <help><![CDATA[ | 51 <help><![CDATA[ |
| 40 .. class:: infomark | 52 .. class:: infomark |
| 41 | 53 |
| 42 **What it does** | 54 **What it does** |
| 43 | 55 |
| 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. | 56 The cosine content of the principal components is a good indicator for determining the quality of the sampling and can be used to determine the convergence of the MD simulation. |
| 45 This tool can calculate the cosine content of a user define PCA projection. | 57 This tool can calculate the cosine content of a user-defined PCA projection. Note: it uses zero-based indexes (i.e. 0 is the first principal component). |
| 46 This tool use zero based indexes (0 is PC1). | 58 |
| 47 | |
| 48 _____ | 59 _____ |
| 49 | 60 |
| 50 | 61 |
| 51 .. class:: infomark | 62 .. class:: infomark |
| 52 | 63 |
| 61 .. class:: infomark | 72 .. class:: infomark |
| 62 | 73 |
| 63 **Output** | 74 **Output** |
| 64 | 75 |
| 65 - The cosine content value. | 76 - The cosine content value. |
| 66 - Tab-separated file of raw data of first three principle component. | 77 - Tab-separated file of raw data of the first three principal components. |
| 67 | 78 |
| 68 ]]></help> | 79 ]]></help> |
| 69 <expand macro="citations"> | 80 <expand macro="citations"> |
| 70 <citation type="doi">10.1103/PhysRevE.65.031910</citation> | 81 <citation type="doi">10.1103/PhysRevE.65.031910</citation> |
| 71 </expand> | 82 </expand> |