Mercurial > repos > marpiech > norwich_tools
changeset 5:fda6e327fac8 draft
planemo upload
| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 07:14:20 -0400 |
| parents | 33606cbc9806 |
| children | 97fb58d6c0cb |
| files | sample.xml smina.xml |
| diffstat | 2 files changed, 11 insertions(+), 146 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sample.xml Mon Aug 29 07:14:20 2016 -0400 @@ -0,0 +1,11 @@ +<tool id="sam_filter_1" name="SAM Filter"> + <command interpreter="python"> + + </command> + <inputs> + + </inputs> + <outputs> + + </outputs> +</tool>
--- a/smina.xml Mon Aug 29 07:05:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,146 +0,0 @@ -<tool id="smina" name="smina" version="0.1.0"> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ - cat $receptor > receptor.pdbqt; - cat $ligand > ligand.pdbqt; - $__tool_directory__/tools/smina/smina.static - --receptor receptor.pdbqt - --ligand ligand.pdbqt - - #if $flex - --flex $flex - #end if - #if $flexres - --flexres $flexres - #end if - #if $flexdist_ligand - --flexdist_ligand $flexdist_ligand - #end if - #if $flexdist - --flexdist $flexdist - #end if - - --center_x $center_x - --center_y $center_y - --center_z $center_z - --size_x $size_x - --size_y $size_y - --size_z $size_z - - #if $autobox_ligand - --autobox_ligand $autobox_ligand - #end if - #if $autobox_add - --autobox_add $autobox_add - #end if - #if $no_lig=="true" - --no_lig - #end if - - --scoring $scoring - #if $custom_scoring - --custom_scoring $custom_scoring - #end if - #if $custom_atoms - --custom_atoms $custom_atoms - #end if - #if $score_only=="true" - --score_only - #end if - #if $local_only=="true" - --local_only - #end if - #if $minimize=="true" - --minimize - #end if - #if $randomize_only=="true" - --randomize_only - #end if - #if $minimize_iters - --minimize_iters $minimize_iters - #end if - - --seed 1000 > $output; - cat $output > /tmp/ouput - ]]> - </command> - <inputs> - <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" /> - <param name="ligand" type="data" format="data" label="ligand: ligand(s)" /> - - <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" /> - <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" /> - <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" /> - <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" /> - - <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" /> - <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" /> - <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" /> - <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" /> - <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" /> - <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" /> - - <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" /> - <param name="autobox_add" type="float" value="4" label="autobox_add: Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" /> - <param name="no_lig" type="select" label="no_lig: no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" optional="true"> - <option value="false" selected="true">Don't use this option</option> - <option value="true">Use this option</option> - </param> - - <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true"> - <option value="default" selected="true">default</option> - <option value="ad4_scoring">ad4_scoring</option> - <option value="dkoes_fast">dkoes_fast</option> - <option value="dkoes_scoring">dkoes_scoring</option> - <option value="dkoes_scoring_old">dkoes_scoring_old</option> - <option value="vina">vina</option> - <option value="vinardo">vinardo</option> - </param> - <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" /> - <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" /> - <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true"> - <option value="false" selected="true">Don't use this option</option> - <option value="true">Use this option</option> - </param> - <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true"> - <option value="false" selected="true">Don't use this option</option> - <option value="true">Use this option</option> - </param> - <param name="minimize" type="select" label="minimize: energy minimization" optional="true"> - <option value="false" selected="true">Don't use this option</option> - <option value="true">Use this option</option> - </param> - <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true"> - <option value="false" selected="true">Don't use this option</option> - <option value="true">Use this option</option> - </param> - <param name="minimize_iters" type="integer" label="minimize_iters: number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" /> - </inputs> - <outputs> - <data name="output" format="data" /> - </outputs> - <tests> - <test> - <param name="receptor" value="smina/protein.pdbqt" /> - <param name="ligand" value="smina/ligand.pdbqt" /> - <param name="center_x" value="11" /> - <param name="center_y" value="90.5" /> - <param name="center_z" value="57.5" /> - <param name="size_x" value="22" /> - <param name="size_y" value="24" /> - <param name="size_z" value="28" /> - <output name="output" file="smina/output_smina" /> - </test> - </tests> - <help> - "Smina help" - </help> - <citations> - <citation type="bibtex"> - @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, } - </citation> - </citations> -</tool>