annotate screen.xml @ 1:05cc95060024 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author bgruening
date Mon, 27 Jul 2020 11:31:39 -0400
parents 2c11d1f9e00b
children
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2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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1 <tool id="ctb_im_screen" name="Screen" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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2 <description>a compound against a library using RDKit</description>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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3 <macros>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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4 <import>macros.xml</import>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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5 <token name="@GALAXY_VERSION@">0</token>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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6 </macros>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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7 <expand macro="requirements" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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8 <command detect_errors="exit_code"><![CDATA[
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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9 screen
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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10 #if $comparator.comparator_opts == 'str':
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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11 --qsmiles '${comparator.input}'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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12 #else:
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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13 --qmolfile ${comparator.input}
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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14 #end if
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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15
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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16 -i '$infile'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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17 -if sdf
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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18 #if $comparator.comparator_opts == 'mol'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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19 --isMol
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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20 #end if
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21 #if $fragment_opts
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22 -f '$fragment_opts'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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23 #end if
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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24 --simmin '$sim_min'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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25 --simmax '$sim_max'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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26 -d '$descriptor_opts'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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27 -m '$metric_opts'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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28 #if $hac_min != ''
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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29 --hacmin '$hac_min'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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30 #end if
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31 #if $hac_max != ''
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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32 --hacmax '$hac_max'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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33 #end if
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34 #if $mw_min != ''
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35 --mwmin '$mw_min'
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36 #end if
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37 #if $mw_max != ''
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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38 --mwmax '$mw_max'
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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39 #end if
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40 --meta
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41 -o outp &>> $logfile && ## the script does not exit 0
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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42 cat outp_metrics.txt &>> $logfile &&
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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43 gzip -d outp.sdf.gz
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44 ]]></command>
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45 <inputs>
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46 <conditional name="comparator">
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47 <param name='comparator_opts' type='select' label="Input type" help="Enter SMILES string or Mol file.">
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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48 <option value='file'>Mol/SDF file</option>
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49 <option value='str'>SMILES string</option>
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50 </param>
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51 <when value='str'>
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52 <param name="input" type="text" label="SMILES input" help="Enter SMILES for a compound.">
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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53 <validator type='length' min='5'/>
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54 </param>
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55 </when>
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56 <when value='file'>
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57 <param name="input" type="data" format="sdf,mol" label="Input" help="Input file in mol/sdf format"/>
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58 </when>
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59 </conditional>
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60 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format, for comparison"/>
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61 <param name="sim_min" type="float" label="Similarity lower cutoff" value="0.7" min="0" max="1" help="(1.0 means identical)"/>
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62 <param name="sim_max" type="float" label="Similarity upper cutoff" value="1.0" min="0" max="1" help="(1.0 means identical)"/>
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63 <param name="descriptor_opts" type="select" label="Type of descriptor or fingerprint" help="Default is rdkit">
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64 <option value="rdkit" selected="true">rdkit</option>
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65 <option value="maccs">maccs</option>
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66 <option value="morgan2">morgan2</option>
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67 <option value="morgan3">morgan3</option>
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68 </param>
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69 <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient">
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70 <option value="tanimoto" selected="true">tanimoto</option>
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71 <option value="asymmetric">asymmetric</option>
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72 <option value="braunblanquet">braunblanquet</option>
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73 <option value="cosine">cosine</option>
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74 <option value="dice">dice</option>
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75 <option value="kulczynski">kulczynski</option>
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76 <option value="mcconnaughey">mcconnaughey</option>
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77 <option value="rogotgoldberg">rogotgoldberg</option>
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78 <option value="russel">russel</option>
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79 <option value="sokal">sokal</option>
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80 </param>
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81 <param name="fragment_opts" type="select" optional="true" label="Find single fragment" help="Find single fragment if more than one (hac = biggest by heavy atom count, mw = biggest by mol weight )">
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82 <option value="hac">Biggest by heavy atom count</option>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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83 <option value="mw">Biggest by molecular weight</option>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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84 </param>
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85 <param name="hac_min" type="integer" optional="true" label="Minimum heavy atom count" help="Minimum number of heavy atoms for a candidate to pass screening"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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86 <param name="hac_max" type="integer" optional="true" label="Maximum heavy atom count" help="Maximum number of heavy atoms for a candidate to pass screening"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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87 <param name="mw_min" type="float" optional="true" label="Minimum molecular weight" help="Minimum molecular weight for a candidate to pass screening"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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88 <param name="mw_max" type="float" optional="true" label="Maximum molecular weight" help="Maximum molecular weight for a candidate to pass screening"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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89 </inputs>
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90
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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91 <expand macro="outputs" />
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92
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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93 <tests>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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94 <test>
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95 <param name='comparator_opts' value="str"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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96 <param name="input" value="C1N=C(C2=CC=CC=C2)C2=CC=CC=C2C2=C1C=NC(NC1=CC=CC=C1)=N2"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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97 <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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98 <param name="descriptor_opts" value="rdkit" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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99 <param name="metric_opts" value="tanimoto" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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100 <param name="sim_min" value="0.45" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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101 <param name="sim_max" value="1.0" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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102 <output name="outfile" ftype='sdf' file="screen_output1.sdf"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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103 </test>
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104 <test>
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105 <param name='comparator_opts' value="file"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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106 <param name="input" value="pyrimethamine.mol" ftype="mol"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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107 <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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108 <param name="descriptor_opts" value="rdkit" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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109 <param name="metric_opts" value="tanimoto" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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110 <param name="sim_min" value="0.7" />
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111 <param name="sim_max" value="0.8" />
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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112 <output name="outfile" ftype='sdf' file="screen_output2.sdf"/>
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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113 </test>
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114 </tests>
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115 <help><![CDATA[
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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116
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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117 .. class:: infomark
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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118
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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119 **What this tool does**
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120
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121 Screen a library against a compound, filtering by fingerprint similarity and a number of other properties.
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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122
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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123 .. class:: infomark
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124
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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125 **Input**
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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126
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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127 | - Compound library in `SDF Format`_
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128 | - Compound to screen against in `SMILES`_ or `SDF Format`_
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129 | - Type of fingerprint
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130 | - Required molecular weight and heavy atom count
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131
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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132 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
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133 .. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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134
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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135 -----
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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136
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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137 .. class:: infomark
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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138
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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139 **Output**
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140
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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141 SD-file of screened compounds, with new 'Similarity' property.
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142
2c11d1f9e00b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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143 ]]></help>
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144 <expand macro="citations" />
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145 </tool>