Mercurial > repos > iuc > rp2paths
annotate rp2paths.xml @ 1:7db06bf670db draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
author | iuc |
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date | Sun, 12 Nov 2023 13:57:52 +0000 |
parents | 1e7007e80a4b |
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1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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3 <macros> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
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4 <token name="@TOOL_VERSION@">1.5.1</token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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5 </macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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6 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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8 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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9 <stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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10 <regex match="TIMEOUT:" level="fatal" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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11 <regex match="ERROR:" level="fatal" /> |
1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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12 <regex match="WARNING:" level="warning" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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13 </stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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14 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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15 mkdir out && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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16 python -m rp2paths all |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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17 '$rp2_pathways' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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18 --outdir out |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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19 --timeout '$adv.timeout' && |
1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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20 cp out/compounds.txt '$compounds' && |
1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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21 if test -f 'out/out_paths.csv'; then |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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22 cp out/out_paths.csv '$master_pathways'; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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23 fi |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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24 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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25 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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26 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/> |
1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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27 <section name="adv" title="Advanced Options" expanded="false"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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28 <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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29 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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30 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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31 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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32 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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33 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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34 </outputs> |
1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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35 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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36 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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37 <!-- test 1: check if identical outputs are produced with default parameters --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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38 <param name="rp2_pathways" value="retropath2_pathways.csv" /> |
1e7007e80a4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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39 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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40 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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41 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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42 </tests> |
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43 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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44 RP2paths |
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45 ======== |
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46 |
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47 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
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48 **RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the "RetroPath2.0 workflow" into individual pathways and enumerate them. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
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49 This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
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50 This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
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51 and outputs the enumerated pathways (using `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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52 |
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53 |
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54 An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://en.wikipedia.org/wiki/Styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
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55 |
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56 |
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57 .. image:: ${static_path}/images/enumerated_pathways.png |
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58 :width: 40 % |
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59 :align: center |
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60 |
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61 | |
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62 |
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63 Input |
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64 ----- |
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65 |
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66 Required information: |
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67 |
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68 * **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis. |
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69 |
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70 Advanced options: |
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71 |
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72 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes. |
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73 |
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74 Output |
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75 ------ |
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76 |
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77 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest. |
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78 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System). |
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79 |
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80 Project Links |
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81 --------------------- |
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82 |
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83 * `GitHub <https://github.com/brsynth/rp2paths>`_ |
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84 |
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85 License |
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86 ------- |
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87 |
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88 `MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_ |
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89 |
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90 Acknowledgments |
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91 --------------- |
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92 |
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93 * Joan Hérisson |
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94 |
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95 ]]></help> |
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96 <citations> |
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97 <citation type="doi">10.1016/j.ymben.2017.12.002</citation> |
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98 </citations> |
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99 </tool> |