Mercurial > repos > tduigou > rp2biosensor

annotate rp2biosensor.xml @ 3:4b2318e9b097 draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Fri, 25 Mar 2022 13:01:27 +0000
parents b0efd4b2ffba
children b9aa7267df42
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1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09">
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2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.1.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python -m rp2biosensor
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11 '$rp2_results'
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12 '$sink_file'
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13 --opath '$html_file'
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14 #if str($adv.json_graph) == "true"
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15 --ojson '$json_file'
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
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20 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
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21 <section name="adv" title="Advanced Options" expanded="false">
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22 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
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23 </section>
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24 </inputs>
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25 <outputs>
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26 <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
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27 <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
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28 <filter> adv['json_graph'] </filter>
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29 </data>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <!-- test 1: check if identical outputs are produced -->
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34 <param name="rp2_results" value="rp2-results-lactate.csv" />
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35 <param name="sink_file" value="sink-h2o2.csv" />
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36 <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 rp2biosensor
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41 ================
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42
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43 Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.
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44
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45 Input
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46 -----
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47
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48 Required:
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49
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50 * **rp2_results**\ : (string) RetroPath2.0 results.
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51 * **sink_file**\ : (string) Sink file used for RetroPath2.0.
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52
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53 Output
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54 ------
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55
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56 * **opath**\ : (string) Output path. Default: biosensor.html.
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57
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58 * **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.
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59
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60 * **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None
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61
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62 Project Links
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63 ------------------
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64
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65 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
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66
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67 Version
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68 ----------
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69
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70 3.1.0
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71
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72 Authors
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73 -------
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74
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75 * **Thomas Duigou**
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76
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77 License
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78 -------
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79
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80 * `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
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81
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82 ]]></help>
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83 </tool>