Mercurial > repos > chemteam > bio3d_dccm
view dccm.xml @ 0:386b4f4b6a85 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
author | chemteam |
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date | Wed, 27 Mar 2019 15:16:19 -0400 |
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children | 18440ff54f63 |
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<tool id="bio3d_dccm" name="DCCM analysis" version="@VERSION@"> <description>Dynamical Cross-Correlation Maps using Bio3D (DCCM)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ Rscript '$__tool_directory__/dccm.R' '$dcdin' '$pdbin' #if $dccm.sele == 'calpha': "string" "calpha" #end if #if $dccm.sele == 'cbeta': "string" '$dccm.cbeta' #end if #if $dccm.sele == 'backbone': "string" "backbone" #end if #if $dccm.sele == 'sidechain': "string" "sidechain" #end if #if $dccm.sele == 'protein': "string" "protein" #end if #if $dccm.sele == 'ligand': "string" "ligand" #end if #if $dccm.sele == 'nucleic': "string" "nucleic" #end if #if $dccm.sele == 'elety': "elety" '$dccm.elety' #end if #if $dccm.sele == 'resid': "resid" '$dccm.resid' #end if #if $dccm.sele == 'segid': "segid" '$dccm.segid' #end if '$output' '$dccm_plot' 2>&1 ]]></command> <inputs> <expand macro="analysis_inputs"/> <conditional name="dccm"> <param name="sele" type="select" label="Select domains"> <option value="calpha">Calpha</option> <option value="cbeta">Cbeta</option> <option value="backbone">Backbone</option> <option value="sidechain">Sidechain</option> <option value="protein">Protein</option> <option value="ligand">Ligand</option> <option value="nucleic">Nucleic Acids</option> <option value="elety">Atom Names</option> <option value="resid">Resid</option> <option value="segid">Segid</option> </param> <when value="calpha"/> <when value="cbeta"/> <when value="backbone"/> <when value="sidechain"/> <when value="protein"/> <when value="ligand"/> <when value="nucleic"/> <when value="elety"> <param name="elety" type="text" value="CA" label="Atom Name"/> </when> <when value="resid"> <param name="resid" type="text" value="BGLC" label="Resid"/> </when> <when value="segid"> <param name="segid" type="text" value="SUBS" label="Segid"/> </when> </conditional> </inputs> <outputs> <data format="tabular" name="output" label="DCCM raw data"/> <data format="png" name="dccm_plot" label="DCCM plot"/> </outputs> <tests> <test> <expand macro="tests_inputs"/> <param name="sele" value="calpha"/> <output name="dccm_plot" file="dccm_plot.png" compare="sim_size" delta="20000" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** The extent to which the atomic fluctuations/displacements of a system are correlated with one another can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The DCCM Analysis tool can plot the atom-wise cross-correlations using the Bio3D package. The negative values (negative correlation) indicate the atoms moves in opposite directions and the positive values (positive correlation) indicate the atoms moves in same directions. _____ .. class:: infomark **Input** - Input file in PDB format - Input file in dcd format _____ .. class:: infomark **Output** - Image (as PNG) of the dccm plot - Tab-separated file of raw data ]]></help> <expand macro="citations" /> </tool>