Mercurial > repos > tduigou > rpcompletion
annotate rpcompletion.xml @ 3:fcc8f3e2d4da draft
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author | tduigou |
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date | Wed, 04 May 2022 10:05:47 +0000 |
parents | d5c53a916005 |
children | e8d56cb2be03 |
rev | line source |
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1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="19.09"> |
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2 <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description> |
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3 <macros> |
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4 <token name="@TOOL_VERSION@">5.12.3</token> |
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5 </macros> |
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6 <requirements> |
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7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> |
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8 </requirements> |
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9 <stdio> |
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10 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" /> |
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11 <exit_code range="2" level="fatal" description="ValueError returned" /> |
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12 </stdio> |
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13 <command detect_errors="exit_code"><![CDATA[ |
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14 python -m rptools.rpcompletion |
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15 '$rp2_pathways' |
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16 '$sink' |
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17 '$rp2paths_compounds' |
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18 '$rp2paths_pathways' |
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19 completed_pathways |
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20 --upper_flux_bound '$adv.upper_flux_bound' |
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21 --lower_flux_bound '$adv.lower_flux_bound' |
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22 --max_subpaths_filter '$adv.max_subpaths_filter' |
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23 ]]></command> |
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24 <inputs> |
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25 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> |
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26 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" /> |
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27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> |
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28 <param name="sink" type="data" format="csv" label="Sink from SBML" /> |
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29 <section name="adv" title="Advanced Options" expanded="false"> |
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30 <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" /> |
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31 <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" /> |
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32 <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" /> |
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33 </section> |
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34 </inputs> |
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35 <outputs> |
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36 <collection name="pathways" type="list" label="${tool.name}"> |
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37 <discover_datasets pattern="(?P<designation>.+)\.xml" format="xml" directory="completed_pathways" visible="false" /> |
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38 </collection> |
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39 </outputs> |
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40 <tests> |
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41 <test> |
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42 <!-- test 1: check if identical outputs are produced with default parameters --> |
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43 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" /> |
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44 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" /> |
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45 <param name="rp2_pathways" value="1-rp2_metnet.csv" /> |
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46 <param name="sink" value="2-sink.csv" /> |
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47 <output_collection name="pathways" type="list"> |
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48 <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/> |
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49 <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/> |
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50 <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/> |
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51 <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/> |
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52 <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/> |
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53 <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/> |
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54 <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/> |
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55 <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/> |
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56 <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/> |
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57 </output_collection> |
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58 </test> |
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59 </tests> |
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60 <help><![CDATA[ |
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61 rpCompletion |
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62 ============ |
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63 |
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64 Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data. |
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65 |
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66 Input |
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67 ----- |
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68 |
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69 Required: |
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70 |
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71 * **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file |
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72 * **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink |
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73 * **rp2paths_compounds**: (string) Path to the rp2paths compounds file |
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74 * **rp2paths_pathways**: (string) Path to the rp2paths pathways file |
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75 * **outdir**: (string) Path to the output directory containing sbml completed pathways |
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76 |
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77 Advanced options: |
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78 |
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79 * **-upper_flux_bound**: (integer, default=9999) Upper flux bound value |
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80 * **-lower_flux_bound**: (integer, default=0) Lower flux bound value |
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81 * **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path |
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82 |
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83 Project Links |
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84 --------------------- |
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85 * `GitHub <https://github.com/brsynth/rptools>`_ |
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86 |
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87 Version |
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88 ---------- |
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89 |
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90 5.12.1 |
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91 |
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92 Authors |
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93 ------- |
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94 |
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95 * **Melchior du Lac** |
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96 * **Joan Hérisson** |
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97 |
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98 Acknowledgments |
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99 --------------- |
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100 |
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101 * Thomas Duigou |
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102 |
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103 Licence |
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104 ------- |
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105 |
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106 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ |
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107 |
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108 ]]></help> |
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109 </tool> |