Mercurial > repos > bgruening > fpocket

annotate dpocket.xml @ 3:4cc9d85c3bae draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
author bgruening
date Fri, 10 Sep 2021 08:20:08 +0000
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3
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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1 <tool id="dpocket" name="dpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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2 <description>to calculate descriptors for protein pockets</description>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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3 <macros>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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4 <import>macros.xml</import>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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5 <token name="@GALAXY_VERSION@">0</token>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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6 </macros>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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7 <expand macro="requirements" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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8 <command detect_errors="exit_code"><![CDATA[
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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9 ## create config file
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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10 #for i in $input:
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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11 ln -s '$i' $i.name.replace(' ', '_') &&
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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12 echo $i.name.replace(' ', '_') >> pdbs.txt &&
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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13 #end for
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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14 paste pdbs.txt '$ligs' > dp_conf.txt &&
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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15
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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16 ## run dpocket
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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17 dpocket
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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18 -f dp_conf.txt
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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19
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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20 ## pocket definition params common with fpocket
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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21 #if $inp.pocket_type == 'channel':
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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22 --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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23 #elif $inp.pocket_type == 'external':
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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24 --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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25 #elif $inp.pocket_type == 'custom':
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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26 --min_alpha_size '$inp.min'
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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27 --max_alpha_size '$inp.max'
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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28 --min_spheres_per_pocket '$inp.i'
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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29 --clustering_distance '$inp.D'
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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30 --clustering_method '$inp.C'
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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31 ##--clustering_measure $inp.e
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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32 #end if
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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33
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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34 ## specific params for explicit pocket definition
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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35 #if $explicit_output.output == "true":
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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36 $explicit_output.interface_definition
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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37 -d $explicit_output.dist
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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38 #end if
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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39
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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40 &&
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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41 ## reformat output files to match Galaxy tabular
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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42 sed -e "s/\s\+/\t/g" dpout_fpocketp.txt > $fpocketp &&
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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43 sed -e "s/\s\+/\t/g" dpout_fpocketnp.txt > $fpocketnp
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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44 #if $explicit_output.output:
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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45 &&
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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46 sed -e "s/\s\+/\t/g" dpout_explicitp.txt > $explicitp
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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47 #end if
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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48
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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49 ]]></command>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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50 <inputs>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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51 <param name="input" type="data" format="pdb" multiple="true" label="Input file" help="Protein structure file(s) (PDB) to search."/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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52 <param name="ligs" type="data" format="txt" label="Ligand codes" help="List of ligand codes (as provided in the PDB files), one per line. The number of codes must match the number of input PDB files."/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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53 <expand macro="inputs" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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54 <!-- <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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55 <option value="fpocketp" selected="true">Pockets which match the ligand position</option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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56 <option value="fpocketnp">Pockets which do NOT match the ligand position</option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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57 <option value="explicitp">Define pocket explicitly as all vertices/atoms within a given distance from the ligand, regardless of what fpocket found. </option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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58 </param> -->
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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59 <conditional name="explicit_output">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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60 <param name="output" type="select" label="Calculate explicit pocket?" help="Define pocket explicitly as all vertices/atoms within a given distance from the ligand, regardless of what fpocket found.">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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61 <option value="true" selected="true">Yes</option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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62 <option value="false">No</option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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63 </param>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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64 <when value="false" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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65 <when value="true">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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66 <param name="interface_definition" type="select" label="Definition of the explicit pocket" help="Protein-ligand explicit interface definition">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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67 <option value="-e" selected="true">All atoms in contact with alpha spheres within a distance threshold from any ligand atom</option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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68 <option value="-E">All atoms within a distance threshold from any ligand atom</option>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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69 </param>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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70 <param name="dist" type="float" value="4.0" min="0" label="Distance threshold for explicit pocket definition (angstroms)" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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71 </when>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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72
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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73 </conditional>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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74 </inputs>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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75
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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76 <outputs>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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77 <data name="fpocketp" format="tabular" label="Pockets matching the submitted ligands"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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78 <data name="fpocketnp" format="tabular" label="Pockets NOT matching the submitted ligands"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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79 <data name="explicitp" format="tabular" label="Pockets defined explicitly based on the submitted ligands">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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80 <filter>explicit_output['output'] == "true"</filter>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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81 </data>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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82 </outputs>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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83
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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84 <tests>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
85 <test expect_num_outputs="3">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
86 <param name="input" ftype="pdb" value="2brc.pdb"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
87 <param name="ligs" ftype="txt" value="ligs.txt"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
88 <param name='pocket_type' value='custom' />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
89 <param name="min" value="4.0"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
90 <param name="max" value="7.0"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
91 <param name="i" value="20" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
92 <param name="D" value="2.0"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
93 <param name="C" value="s" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
94 <param name="interface_definition" value="-E" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
95 <param name="dist" value="5" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
96 <param name='explicit_output' value='true' />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
97 <output name="fpocketp" ftype="tabular">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
98 <assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
99 <has_n_columns n="57" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
100 <has_n_lines n="2" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
101 <has_text_matching expression="2brc.pdb\s+CT5\s+31.15\s+1\s+1.07\s+0.77\s+1.00\s+1\s+1.54"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
102 <has_text_matching expression="6.50\s+0.96\s+0.44\s+14.39\s+23.64\s+12.20\s+42.27\s+15.29\s+2\s+1\s+0\s+2"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
103 </assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
104 </output>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
105 <output name="fpocketnp" ftype="tabular">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
106 <assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
107 <has_n_columns n="57" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
108 <has_n_lines n="2" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
109 <has_text_matching expression="2brc.pdb\s+CT5\s+0.00\s+0\s+17.62\s+0.00\s+0.00\s+0\s+-1.25"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
110 <has_text_matching expression="4.36\s+0.69\s+0.00\s+4.37\s+31.43\s+42.10\s+33.81\s+17.20\s+5\s+0\s+1\s+1"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
parents:
diff changeset
111 </assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
112 </output>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
113 <output name="explicitp" ftype="tabular">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
114 <assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
115 <has_n_columns n="57" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
116 <has_n_lines n="2" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
117 <has_text_matching expression="2brc.pdb\s+CT5\s+100.00\s+1\s+0.00\s+1.00\s+1.00\s+1\s+2.00"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
118 <has_text_matching expression="11.97\s+0.00\s+0.00\s+107.35\s+56.94\s+61.01\s+57.97\s+34.40\s+3\s+2\s+0\s+2"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
119 </assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
120 </output>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
121 </test>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
122 <test expect_num_outputs="3">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
123 <param name="input" ftype="pdb" value="2brc.pdb,1L83.pdb"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
124 <param name="ligs" ftype="txt" value="ligs2.txt"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
125 <param name='pocket_type' value='small_mol' />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
126 <param name='explicit_output' value='false' />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
127 <output name="fpocketp" ftype="tabular">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
128 <assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
129 <has_n_columns n="57" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
130 <has_n_lines n="3" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
131 <has_text_matching expression="2brc.pdb\s+CT5\s+38.60\s+1\s+0.54\s+0.46\s+0.80\s+0\s+0.67"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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132 <has_text_matching expression="1L83.pdb\s+BNZ\s+100.00\s+1\s+0.83\s+1.00\s+0.85\s+1\s+1.81"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
133 </assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
134 </output>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
135 <output name="fpocketnp" ftype="tabular">
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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diff changeset
136 <assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
137 <has_n_columns n="57" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
138 <has_n_lines n="19" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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139 <has_text_matching expression="2brc.pdb\s+CT5\s+0.00\s+0\s+17.15\s+0.00\s+0.00\s+0\s+-1.25"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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140 <has_text_matching expression="29.17\s+4.03\s+0.65\s+11.05\s+0.65\s+0.14\s+13.17\s+29.13\s+19.24"/>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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diff changeset
141 </assert_contents>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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142 </output>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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143 </test>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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diff changeset
144 </tests>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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145 <help><![CDATA[
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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146
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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147 Calculate descriptors (i.e. featurize) 'pockets' in a protein structure, using the
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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148 dpocket module of the fpocket software.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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149
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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150 To use, upload one or more protein structures in PDB format and select the type of pocket to
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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151 detect. 'Custom options' can also be selected - this exposes all internal fpocket
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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152 parameters. Using this option requires some knowledge of the fpocket prediction
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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153 algorithm. Please consult the cited publications for more details.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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154
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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155 In addition, a list of ligand identifiers should be provided as a text file, one per line and
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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156 one for each of the protein structures.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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157
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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158
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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159 -----
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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160
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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161 .. class:: infomark
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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162
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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163 **Input**
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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164
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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165 - One or more protein structures in PDB format. If using multiple structures, submitting them as a dataset collection is recommended to ensure ordering is preserved.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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166 - Text file with ligand identifiers, matching the ligand code in the PDB files. One identifier should be listed per line and one per PDB file.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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167
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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168 -----
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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169
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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170 .. class:: infomark
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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171
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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172 **Output**
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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173
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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174 - Tabular file with descriptors of pockets matching the positions of the input ligands.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
bgruening
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175 - Tabular file with descriptors of pockets which do NOT match the positions of the input ligands.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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176 - (Optional) Tabular file with descriptors of pockets which are explicitly defined by the positions of the input ligands.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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177
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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178 Each tabular file contains 57 columns (55 descriptors, plus protein and ligand names), a header line, and
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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179 one row per pocket found.
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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180
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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181 ]]></help>
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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182 <expand macro="citations" />
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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183 </tool>