Mercurial > repos > chemteam > mdanalysis_cosine_analysis
view pca_cosine.xml @ 3:9a3a1f698fc6 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author | chemteam |
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date | Wed, 20 May 2020 13:03:58 -0400 |
parents | d18e7db42633 |
children | a842da7ef42b |
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<tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@"> <description>- measure the cosine content of the PCA projection</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/pca_cosine.py' --itraj '$trajin' --istr '$strin' --itrajext '$trajin.ext' --istrext '$strin.ext' --icomponents '$components' --iindex '$index' --output '$output' --cosout '$cosout' 2>&1 ]]></command> <inputs> <expand macro="analysis_inputs"/> <param name="components" type="integer" value="3" label="Number of components"/> <param name="index" type="integer" value="0" label="The index of the PCA component projection to be analyzed"/> </inputs> <outputs> <data format="tabular" name="output" label="PCA Analysis raw data"/> <data format="txt" name="cosout" label="Cosine content of the PCA projection"/> </outputs> <tests> <test> <expand macro="tests_inputs"/> <param name="components" value="3"/> <param name="index" value="0"/> <output name="cosout"> <assert_contents> <has_text text="0.5832533" /> </assert_contents> </output> </test> <test> <expand macro="tests_inputs_gmx"/> <param name="components" value="3"/> <param name="index" value="0"/> <output name="cosout"> <assert_contents> <has_text text="0.583" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** 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. 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). _____ .. class:: infomark **Input** - Trajectory file (DCD). - PDB file. _____ .. class:: infomark **Output** - The cosine content value. - Tab-separated file of raw data of the first three principal components. ]]></help> <expand macro="citations"> <citation type="doi">10.1103/PhysRevE.65.031910</citation> </expand> </tool>