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annotate rpreport.xml @ 2:432623008c84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:10:56 +0000
parents a1764894d6ca
children a03d4c0887cc
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1 <tool id="rptools_rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Explore the main characteristics of pathways predicted with RetroPath suite</description>
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3 <macros>
2
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4 <import>macros.xml</import>
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5 </macros>
2
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if str($input_type_conditional.input_type) == "sbml":
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9 #set input_folder="tmp_folder"
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10 mkdir -p '$input_folder' &&
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11 #for $input in $input_type_conditional.input_sbml.keys():
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12 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input' &&
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13 #end for
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14 python -m rptools.rpreport -d '$input_folder'
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15 #elif str($input_type_conditional.input_type) == "tar":
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16 python -m rptools.rpreport '${input_type_conditional.input_tar}'
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17 #end if
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18 '$html_file.files_path'
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19 && cp '$html_file.files_path'/index.html '$html_file'
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20 ]]></command>
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21 <inputs>
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22 <conditional name="input_type_conditional">
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23 <param name="input_type" type="select" label="Source SBML format">
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24 <option value="tar" selected="True">TAR</option>
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25 <option value="sbml">Collection</option>
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26 </param>
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27 <when value="tar">
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28 <param name="input_tar" type="data" format="tar" label="Source SBML" help="rpSBML file(s) containing pathways predicted with RetroPath suite in TAR format"/>
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29 </when>
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30 <when value="sbml">
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31 <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" help="Collection of rpSBML files containing pathways predicted with RetroPath suite"/>
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data name="html_file" format="html" label="Pathways HTML Report"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <!-- test 1: check if identical html output is produced (tar input) -->
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41 <conditional name="input_type_conditional">
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42 <param name="input_type" value="tar"/>
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43 <param name="input_tar" value="input_rpSBML.tar" />
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44 </conditional>
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45 <output name="html_file" file="rpreport_output.html" compare="diff"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 rpReport
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50 =========
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51
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52 Generates HTML pages to explore the main characteristics (thermodynamics,
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53 fluxes, number of metabolic steps, reaction rule score) of pathways predicted
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54 with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
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55
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56
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57 Input
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58 -----
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59
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60 Required:
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61
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62 * **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite.
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63
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64 Output
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65 ------
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66
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67 * **Pathways HTML Report**: Pathways HTML Report
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68 ]]></help>
2
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69 <expand macro="creator"/>
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70 <citations>
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71 <citation type="doi">10.1038/s41467-022-32661-x</citation>
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72 </citations>
0
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73 </tool>