Mercurial > repos > bgruening > ctb_im_cluster_butina

annotate cluster_butina.xml @ 1:65316a9205f5 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author bgruening
date Mon, 27 Jul 2020 11:33:10 -0400
parents ad2b25cca758
children
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ad2b25cca758 "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_cluster_butina" name="Butina Cluster" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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2 <description>using RDKit</description>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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3 <macros>
ad2b25cca758 "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>
ad2b25cca758 "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>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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6 </macros>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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7 <expand macro="requirements" />
ad2b25cca758 "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[
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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9 cluster_butina
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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10 -i '$infile'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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11 -if sdf
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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12 -t '$threshold'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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13 -d '$descriptor_opts'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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14 -m '$metric_opts'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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15 #if $number != ''
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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16 -n '$number'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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17 #end if
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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18 -e '$exclude'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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19 #if $fragment_opts:
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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20 --fragment-method '$fragment_opts'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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21 #end if
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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22 #if $field_conditional.use_field == 't':
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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23 #if $field_conditional.field:
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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24 -f '$field_conditional.field'
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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25 $field_conditional.field_opts
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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26 #end if
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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27 #end if
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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28 $output_fragment
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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29 --meta
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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30 -o outp
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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31 -of sdf &>> $logfile &&
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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32 cat outp_metrics.txt &>> $logfile &&
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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33 gzip -d outp.sdf.gz
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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34 ]]></command>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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35 <inputs>
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36 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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37 <param name="threshold" min="0" max="1" type="float" value="0.7" label="Threshold" help="Similarity clustering threshold (1.0 means identical)"/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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38 <param name="descriptor_opts" type="select" label="Descriptor Options" help="Descriptor or fingerprint type (default rdkit)">
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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39 <option value="rdkit" selected="true">rdkit</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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40 <option value="maccs">maccs</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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41 <option value="morgan2">morgan2</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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42 <option value="morgan3">morgan3</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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43 </param>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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44 <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient">
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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45 <option value="tanimoto" selected="true">tanimoto</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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46 <option value="asymmetric">asymmetric</option>
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47 <option value="braunblanquet">braunblanquet</option>
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48 <option value="cosine">cosine</option>
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49 <option value="dice">dice</option>
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50 <option value="kulczynski">kulczynski</option>
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51 <option value="mcconnaughey">mcconnaughey</option>
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52 <option value="rogotgoldberg">rogotgoldberg</option>
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53 <option value="russel">russel</option>
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54 <option value="sokal">sokal</option>
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55 </param>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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56 <param name="number" type="integer" optional="true" label="Maximum number for diverse subset selection" help="Maximum number to pick for diverse subset selection. Leave blank for no maximum."/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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57 <param name="exclude" min="0" max="1" type="float" value="0.9" label="Exclude threshold" help="Threshold for excluding structures in diverse subset selection (1.0 means identical)"/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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58 <param name="fragment_opts" type="select" optional="true" label="Find single fragment" help="Find single fragment if more than one">
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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59 <option value="hac" selected="true">Biggest by heavy atom count</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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60 <option value="mw">Biggest by molecular weight</option>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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61 </param>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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62 <param name="output_fragment" type="boolean" label="Output Fragment" truevalue="--output-fragment" falsevalue="" help="Output the biggest fragment rather than the original molecule"/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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63 <conditional name="field_conditional">
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64 <param name="use_field" type="boolean" label="Use field" truevalue="t" falsevalue="f" help="Use a field to optimize diverse subset selection"/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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65 <when value="t">
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66 <param name="field" type="text" label="Field" help="Field to use to optimise diverse subset selection"/>
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67 <param name="field_opts" type="select" label="Field options" help="pick lowest or highest value specified by the 'field' component">
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68 <option value="--min" selected="true">min</option>
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69 <option value="--max">max</option>
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70 </param>
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71 </when>
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72 <when value="f" />
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73 </conditional>
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74 </inputs>
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75
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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76 <expand macro="outputs" />
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77 <tests>
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78 <test>
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79 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
ad2b25cca758 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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80 <param name="descriptor_opts" value="rdkit"/>
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81 <param name="metric_opts" value="tanimoto"/>
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82 <param name="threshold" value="0.6"/>
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83 <param name="fragment_opts" value="hac"/>
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84 <output name="outfile" ftype='sdf' file="cluster_butina_output1.sdf"/>
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85 <output name="logfile">
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86 <assert_contents>
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87 <has_text text="Found 30 clusters"/>
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88 </assert_contents>
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89 </output>
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93
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94 .. class:: infomark
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95
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96 **What this tool does**
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97
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98 This tool performs Butina clustering for a set of input molecules, using the chemistry toolkit RDKit, and returns results in SDF format.
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99
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100
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101 -----
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102
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103 .. class:: infomark
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104
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105 **Input**
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106
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107 | - Molecules in `SDF format`_
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108 | - A number of other parameters can be set, including the fingerprint type and the similarity metric to use.
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109
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110 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
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111
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112
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113 -----
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114
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115 .. class:: infomark
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116
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117 **Output**
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118
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119 SD file containing clusters.
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120
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121 ]]></help>
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122 <expand macro="citations"/>
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123 </tool>