Mercurial > repos > guerler > spring_model_all

annotate macros.xml @ 1:e56e0f4c84fb draft

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"planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
author guerler
date Mon, 29 Mar 2021 21:50:37 +0000
parents 64cb5fab9c60
children
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="@TOOL_VERSION@">springsuite</requirement>
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5 <yield />
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6 </requirements>
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7 </xml>
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8 <token name="@TOOL_VERSION@">0.2</token>
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9 <token name="@VERSION_SUFFIX@">0</token>
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10
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11 <xml name="ffindex_single_inputs">
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12 <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
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13 <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
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14 </xml>
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15
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16 <xml name="ffindex_single_inputs_hhr">
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17 <param name="ffdata" type="data" format="ffdata" label="HHR Database" help="Database Data file." />
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18 <param name="ffindex" type="data" format="ffindex" label="HHR Database Index" help="Database Index file." />
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19 </xml>
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20
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21 <xml name="citations">
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22 <citations>
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23 <citation type="doi">10.1021/ci300579r</citation>
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24 </citations>
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25 </xml>
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26 <xml name="logfile">
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27 <param name="logfile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file" />
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28 </xml>
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29
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30 <xml name="pdb_source">
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31 <conditional name="pdb_source">
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32 <param name="pdb_source_selector" type="select" label="Custom or built-in PDB" help="Built-ins have been indexed using ffindex">
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33 <option value="indexed" selected="true">Use a built-in index</option>
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34 <option value="history">Use a PDB index from history</option>
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35 </param>
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36 <when value="indexed">
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37 <param name="pdb" type="select" label="Select PDB database" help="">
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38 <options from_data_table="ffindex_indices">
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39 <filter type="sort_by" column="0" />
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40 <filter type="static_value" column="3" value="pdb" />
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41 <validator type="no_options" message="No indices are available" />
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42 </options>
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43 </param>
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44 <param name="zipped" type="select" label="Zipped entries in PDB database?" help="">
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45 <option value="" selected="true">No</option>
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46 <option value="gz">Yes</option>
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47 </param>
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48 </when>
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49 <when value="history">
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50 <expand macro="ffindex_single_inputs" />
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51 </when>
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52 </conditional>
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53 </xml>
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54 <xml name="hhr_source">
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55 <conditional name="hhr_source">
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56 <param name="hhr_source_selector" type="select" label="Custom or built-in HHR index" help="Built-ins have been indexed using ffindex">
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57 <option value="indexed" selected="true">Use a built-in index</option>
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58 <option value="history">Use a HHR index from history</option>
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59 </param>
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60 <when value="indexed">
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61 <param name="hhr" type="select" label="Select HHR database" help="">
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62 <options from_data_table="ffindex_indices">
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63 <filter type="sort_by" column="0" />
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64 <filter type="static_value" column="3" value="hhr" />
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65 <validator type="no_options" message="No indices are available" />
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66 </options>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <expand macro="ffindex_single_inputs_hhr" />
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71 </when>
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72 </conditional>
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73 </xml>
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74
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75 <token name="@pdb_source@">
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76 #if $pdb_source.pdb_source_selector == 'indexed':
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77 -d '${pdb_source.pdb.fields.path}.ffdata'
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78 -i '${pdb_source.pdb.fields.path}.ffindex'
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79 -z '$pdb_source.zipped'
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80 #else
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81 -d '$pdb_source.ffdata'
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82 -i '$pdb_source.ffindex'
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83 #end if
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84 </token>
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85 <token name="@hhr_source@">
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86 #if $hhr_source.hhr_source_selector == 'indexed':
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87 -dh '${hhr_source.hhr.fields.path}.ffdata'
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88 -ih '${hhr_source.hhr.fields.path}.ffindex'
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89 #else
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90 -dh '$hhr_source.ffdata'
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91 -ih '$hhr_source.ffindex'
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92 #end if
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93 </token>
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94 </macros>