Mercurial > repos > tduigou > rp2biosensor
annotate rp2biosensor.xml @ 3:4b2318e9b097 draft
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author | tduigou |
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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> |