Mercurial > repos > tduigou > rpviz

annotate rpviz.xml @ 0:ea2ca40a24c5 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 17:40:42 +0000
parents
children 8057fdd27860
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1 <tool id="rpviz" name="Visualize pathways" version="5.10.0">
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2 <description>Visualize pathways from the RetroPath Suite</description>
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3 <requirements>
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4 <requirement type="package" version="5.10.0">rptools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #set input_folder="input_folder"
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8 mkdir -p '$input_folder';
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9 #if str($input_type_conditional.input_type) == "sbml":
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10 #for $input in $input_type_conditional.input_sbml.keys():
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11 ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml';
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12 #end for
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13 python -m rptools.rpviz '$input_folder'
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14 #elif str($input_type_conditional.input_type) == "tar":
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15 python -m rptools.rpviz '${input_type_conditional.input_tar}'
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16 #elif str($input_type_conditional.input_type) == "single_sbml":
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17 ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}';
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18 python -m rptools.rpviz '$input_folder'
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19 #end if
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20 'out'
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21 #if $adv.cofactor_file
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22 --cofactor '$adv.cofactor_file'
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23 #end if
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24 --autonomous_html '$html_file';
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25 rm -fr '$input_folder';
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26 ]]></command>
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27 <inputs>
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28 <conditional name="input_type_conditional">
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29 <param name="input_type" type="select" label="Source SBML format">
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30 <option value="tar" selected="True">TAR</option>
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31 <option value="sbml">Collection</option>
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32 <option value="single_sbml">single SBML</option>
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33 </param>
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34 <when value="tar">
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35 <param name="input_tar" type="data" format="tar" label="Source SBML" />
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36 </when>
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37 <when value="sbml">
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38 <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" />
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39 </when>
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40 <when value="single_sbml">
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41 <param name="input_single_sbml" type="data" format="xml" label="Source SBML" />
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42 </when>
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43 </conditional>
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44 <section name="adv" title="Advanced Options" expanded="false">
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45 <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" />
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <!-- test 1: check if identical html output is produced (single sbml input) -->
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54 <conditional name="input_type_conditional">
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55 <param name="input_type" value="single_sbml"/>
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56 <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
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57 </conditional>
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58 <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/>
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59 </test>
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60 <test>
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61 <!-- test 2: check if identical html output is produced (tar input) -->
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62 <conditional name="input_type_conditional">
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63 <param name="input_type" value="tar"/>
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64 <param name="input_tar" value="as_tar_inputs.tgz" />
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65 </conditional>
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66 <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 RPVIZ
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71 ================
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72 Visualize pathways from the RetroPath Suite
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73
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74 Input
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75 -----
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76
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77 * **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder.
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78
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79 Output
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80 ------
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81
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82 * **output_folder**\ : (string) Output folder to be used. If it does not exist, an attempt will be made to create it.It the creation of the folder fails, IOError will be raised.
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83 * **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies.
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84
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85 Project Links
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86 ------------------
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87
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88 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_
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89
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90 Version
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91 ----------
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92
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93 5.10.0
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94
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95 License
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96 -------
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97
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98 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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99
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100 ]]></help>
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101 </tool>