| Previous changeset 4:4354d92dc1aa (2019-04-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" |
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modified:
macros.xml rmsf.xml |
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| diff -r 4354d92dc1aa -r 6bcb804a54c3 macros.xml --- a/macros.xml Wed Apr 03 15:45:27 2019 -0400 +++ b/macros.xml Mon Oct 07 12:45:26 2019 -0400 |
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| @@ -1,14 +1,14 @@ <macros> - <token name="@VERSION@">2.3</token> + <token name="@VERSION@">2.3.4</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.3_3">r-bio3d</requirement> + <requirement type="package" version="2.3_4">r-bio3d</requirement> <yield/> </requirements> </xml> <xml name="analysis_inputs"> - <param format="dcd" name="dcdin" type="data" label="dcd trajectory input"/> - <param format="pdb" name="pdbin" type="data" label="pdb input"/> + <param format="dcd" name="dcdin" type="data" label="DCD trajectory input"/> + <param format="pdb" name="pdbin" type="data" label="PDB input"/> <yield/> </xml> <xml name="tests_inputs"> |
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| diff -r 4354d92dc1aa -r 6bcb804a54c3 rmsf.xml --- a/rmsf.xml Wed Apr 03 15:45:27 2019 -0400 +++ b/rmsf.xml Mon Oct 07 12:45:26 2019 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@"> - <description>rmsf using Bio3D</description> + <description> using Bio3D</description> <macros> <import>macros.xml</import> </macros> @@ -74,20 +74,20 @@ <expand macro="analysis_inputs"/> <conditional name="rmsf"> <param name="sele" type="select" label="Select domains"> - <option value="calpha">Calpha</option> - <option value="cbeta">Cbeta</option> + <option value="calpha">C-alpha</option> + <option value="cbeta">C-beta</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="nucleic">Nucleic acids</option> <option value="loop">Loop</option> <option value="water">Water</option> <option value="hyd">Hydrogens</option> - <option value="noh">Non Hydrogens</option> - <option value="elety">Atom Names</option> - <option value="resid">Resid</option> - <option value="segid">Segid</option> + <option value="noh">Non-hydrogens</option> + <option value="elety">Atom names</option> + <option value="resid">Residue ID</option> + <option value="segid">Segment ID</option> </param> <when value="calpha"> </when> @@ -104,8 +104,8 @@ <when value="nucleic"> </when> <when value="loop"> - <param name="res1" type="text" label="Resid of the loop starting residue"/> - <param name="res2" type="text" label="Resid of the loop ending residue"/> + <param name="res1" type="text" label="ID of the residue at the start of the loop"/> + <param name="res2" type="text" label="ID of the residue at the end of the loop"/> </when> <when value="water"> </when> @@ -114,25 +114,31 @@ <when value="noh"> </when> <when value="elety"> - <param name="elety" type="text" value="CA" label="Atom Name"/> + <param name="elety" type="text" value="CA" label="Atom name"/> </when> <when value="resid"> - <param name="resid" type="text" value="BGLC" label="Resid"/> + <param name="resid" type="text" value="BGLC" label="Residue ID"/> </when> <when value="segid"> - <param name="segid" type="text" value="SUBS" label="Segid"/> + <param name="segid" type="text" value="SUBS" label="Segment ID"/> </when> </conditional> </inputs> <outputs> - <data format="tabular" name="output" label="rmsf raw data"/> - <data format="png" name="rmsf_plot" label="rmsf plot"/> + <data format="tabular" name="output" label="RMSF raw data"/> + <data format="png" name="rmsf_plot" label="RMSF plot"/> </outputs> <tests> <test> <expand macro="tests_inputs"/> <param name="sele" value="calpha"/> - <output name="output" file="rmsf_raw_data.tabular" /> + <output name="output" > + <assert_contents> + <has_line_matching expression="1\t0.297.*" /> + <has_line_matching expression="418\t0.410.*" /> + <has_line_matching expression="433\t0.300.*" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ @@ -141,8 +147,9 @@ **What it does** -The Root Mean Square Fluctuation (RMSF) conformational variance that analysis can analyze the -portions of structure that are fluctuating from their mean structure the most (or least). This tool can calculate and plot the RMSF of the selected section. +The Root Mean Square Fluctuation (RMSF) provides a measure of conformational variance i.e. which +portions of structure are fluctuating from their mean structure the most (or least). +This tool can calculate and plot the RMSF of the selected section of the protein (or other molecule). _____ @@ -159,7 +166,7 @@ **Output** - - Image (as PNG) of the rmsf plot + - Image (as PNG) of the RMSF plot - Tab-separated file of raw data |