Mercurial > repos > chemteam > bio3d_dccm
diff 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 |
parents | |
children | 18440ff54f63 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dccm.xml Wed Mar 27 15:16:19 2019 -0400 @@ -0,0 +1,131 @@ +<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> +