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rpcompletion input extension #192

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merged 4 commits into from
Jul 24, 2024
Merged

rpcompletion input extension #192

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ec0ce2b
fix(tools): rptools rpcompletion, mv input extension
guillaume-gricourt Jul 23, 2024
024016d
fix(tools): rptools, rm bad urls
guillaume-gricourt Jul 23, 2024
468e17f
fix(tools): rptools rpcompletion, mv test case
guillaume-gricourt Jul 24, 2024
e210c6d
fix(tools): rptools rpcompletion, mv test case
guillaume-gricourt Jul 24, 2024
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6 changes: 3 additions & 3 deletions tools/rptools/rpcompletion.xml
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Expand Up @@ -22,7 +22,7 @@
]]></command>
<inputs>
<param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
<param name="rp2paths_compounds" type="data" format="csv" label="RP2paths compounds" />
<param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
<param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
<param name="sink" type="data" format="csv" label="Sink from SBML" />
<section name="adv" title="Advanced Options" expanded="false">
Expand All @@ -43,14 +43,14 @@
<param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
<param name="rp2_pathways" value="1-rp2_metnet.csv" />
<param name="sink" value="2-sink.csv" />
<output_collection name="pathways" type="list" count="9"/>
<output_collection name="pathways" type="list" count="10"/>
</test>
</tests>
<help><![CDATA[
rpCompletion
============

Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ 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.
Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ 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.

Input
-----
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1 change: 0 additions & 1 deletion tools/rptools/rpextractsink.xml
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Expand Up @@ -69,7 +69,6 @@ Output
<citation type="doi">10.1038/nbt1156</citation>
<citation type="doi">10.1016/j.ymben.2017.12.002</citation>
<citation type="doi">10.1186/1752-0509-7-74</citation>
<citation type="doi">10.1093/bioinformatics/btn051</citation>
<citation type="doi">10.1038/s41467-022-32661-x</citation>
</citations>
</tool>
2 changes: 1 addition & 1 deletion tools/rptools/rpreport.xml
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Expand Up @@ -51,7 +51,7 @@ rpReport

Generates HTML pages to explore the main characteristics (thermodynamics,
fluxes, number of metabolic steps, reaction rule score) of pathways predicted
with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
with `RetroPath suite <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_.


Input
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2 changes: 1 addition & 1 deletion tools/rptools/rpviz.xml
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Expand Up @@ -79,7 +79,7 @@
RPVIZ
=====

Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
Visualize pathways from the `RetroPath Suite <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_.

Input
-----
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