Mercurial > repos > chemteam > bio3d_pca
diff pca.xml @ 0:f56fb2762abb draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
author | chemteam |
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date | Mon, 08 Oct 2018 12:49:36 -0400 |
parents | |
children | 54dd1596e04e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pca.xml Mon Oct 08 12:49:36 2018 -0400 @@ -0,0 +1,151 @@ +<tool id="bio3d_pca" name="PCA" version="@VERSION@"> + <description>Principle component analysis using Bio3D</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> +<![CDATA[ + Rscript '$__tool_directory__/pca.R' + '$dcdin' + '$pdbin' + '$method' + #if $pca.sele == 'calpha': + "string" + "calpha" + #end if + #if $pca.sele == 'cbeta': + "string" + '$pca.cbeta' + #end if + #if $pca.sele == 'backbone': + "string" + "backbone" + #end if + #if $pca.sele == 'sidechain': + "string" + "sidechain" + #end if + #if $pca.sele == 'protein': + "string" + "protein" + #end if + #if $pca.sele == 'ligand': + "string" + "ligand" + #end if + #if $pca.sele == 'nucleic': + "string" + "nucleic" + #end if + #if $pca.sele == 'elety': + "elety" + '$pca.elety' + #end if + #if $pca.sele == 'resid': + "resid" + '$pca.resid' + #end if + #if $pca.sele == 'segid': + "segid" + '$pca.segid' + #end if + '$output' + '$pca_plot' + '$pca_cluster' + '$pc1_rmsf' + 2>&1 +]]></command> + <inputs> + <expand macro="analysis_inputs"/> + <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" + label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" /> + <conditional name="pca"> + <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> + <when value="cbeta"> + </when> + <when value="backbone"> + </when> + <when value="sidechain"> + </when> + <when value="protein"> + </when> + <when value="ligand"> + </when> + <when value="nucleic"> + </when> + <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="PCA raw data"/> + <data format="png" name="pca_plot" label="PCA plot"/> + <data format="png" name="pca_cluster" label="PCA Cluster Plot"/> + <data format="png" name="pc1_rmsf" label="PC1 on RMSF"/> + </outputs> + <tests> + <test> + <expand macro="tests_inputs"/> + <param name="method" value="false"/> + <param name="sele" value="calpha"/> + <output name="output"> + <assert_contents> + <has_n_columns n="4" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +PCA can be used to determine the relationship between statistically meaningful conformations (major global motions) +sampled during the trajectory. + +_____ + + +.. class:: infomark + +**Input** + + - Input file in PDB format + - Input file in dcd format + +_____ + + +.. class:: infomark + +**Output** + + - Image (as PNG) of the pca plot + - Image (as PNG) of the pca clusterd plot + - Image (as PNG) of the PC1 plotted on RMSF + - Tab-separated file of raw data + + ]]></help> + <expand macro="citations" /> +</tool>