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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:39:23 +0000
parents ea2ca40a24c5
children
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1 <tool id="rpviz" name="Visualize pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Visualize pathways from the RetroPath Suite</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">6.0.1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set input_folder="input_folder"
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12 mkdir -p '$input_folder' &&
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13 #if str($input_type_conditional.input_type) == "sbml":
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14 #for $input in $input_type_conditional.input_sbml.keys():
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15 ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml' &&
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16 #end for
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17 python -m rptools.rpviz '$input_folder'
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18 #elif str($input_type_conditional.input_type) == "tar":
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19 python -m rptools.rpviz '${input_type_conditional.input_tar}'
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20 #elif str($input_type_conditional.input_type) == "single_sbml":
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21 ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}' &&
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22 python -m rptools.rpviz '$input_folder'
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23 #end if
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24 'out'
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25 #if $adv.cofactor_file
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26 --cofactor '$adv.cofactor_file'
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27 #end if
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28 --autonomous_html '$html_file' &&
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29 rm -fr '$input_folder'
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30 ]]></command>
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31 <inputs>
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32 <conditional name="input_type_conditional">
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33 <param name="input_type" type="select" label="Source SBML format">
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34 <option value="tar" selected="True">TAR</option>
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35 <option value="sbml">Collection</option>
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36 <option value="single_sbml">single SBML</option>
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37 </param>
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38 <when value="tar">
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39 <param name="input_tar" type="data" format="tar" label="Source SBML" />
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40 </when>
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41 <when value="sbml">
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42 <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" />
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43 </when>
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44 <when value="single_sbml">
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45 <param name="input_single_sbml" type="data" format="sbml" label="Source SBML" />
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46 </when>
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47 </conditional>
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48 <section name="adv" title="Advanced Options" expanded="false">
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49 <param name="cofactor_file" type="data" format="tsv" optional="true" label="Cofactor file" help="File listing structures to consider as cofactors."/>
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50 </section>
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51 </inputs>
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52 <outputs>
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53 <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <!-- test 1: check if identical html output is produced (single sbml input) -->
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58 <conditional name="input_type_conditional">
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59 <param name="input_type" value="single_sbml"/>
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60 <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
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61 </conditional>
1
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62 <output name="html_file" >
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63 <assert_contents>
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64 <has_size value="1296252" delta="100" />
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65 </assert_contents>
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66 </output>
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67 </test>
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68 <test>
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69 <!-- test 2: check if identical html output is produced (tar input) -->
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70 <conditional name="input_type_conditional">
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71 <param name="input_type" value="tar"/>
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72 <param name="input_tar" value="as_tar_inputs.tgz" />
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73 </conditional>
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74 <output name="html_file" >
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75 <assert_contents>
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76 <has_size value="1604488" delta="100" />
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 RPVIZ
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83 ================
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84
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85 Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
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86
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87 Input
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88 -----
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89
1
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90 Required:
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91
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92 * **Source SBML**\ : Input file containing rpSBML files in a tar archive, collection or single file.
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93
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94 Optional:
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95
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96 * **Cofactor file**\ : File listing structures to consider as cofactors.
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97
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98 Output
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99 ------
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100
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101 * **Pathways Visualization**\ : HTML output for pathway's visualization.
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102
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103 Project Links
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104 ------------------
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105
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106 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_
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107
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108 License
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109 -------
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110
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111 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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112
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113 ]]></help>
1
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114 <creator>
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115 <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" />
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116 </creator>
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117 </tool>