Mercurial > repos > tduigou > selenzy
diff selenzy.xml @ 1:34a9d136a5bf draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
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date | Tue, 08 Feb 2022 11:12:28 +0000 |
parents | 481f7c35323d |
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--- a/selenzy.xml Wed Dec 15 13:59:04 2021 +0000 +++ b/selenzy.xml Tue Feb 08 11:12:28 2022 +0000 @@ -1,27 +1,34 @@ -<tool id="selenzy-wrapper" name="Selenzyme" version="0.1.0"> +<tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@" profile="19.09"> <description>Performs enzyme selection from a reaction query</description> - <requirements> - <requirement type="package" version="0.1.0">selenzy_wrapper</requirement> + <macros> + <token name="@TOOL_VERSION@">0.2.0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - python -m selenzy_wrapper '$pathway' '$uniprot_ids' + python -m selenzy_wrapper '$pathway' '$uniprot_ids' --nb_targets '$adv.nb_targets' --d '$adv.direction' #if str($adv.NoMSA) == "false": --NoMSA #end if - --taxonIDs '$adv.taxonIDs' + --host_taxID '$adv.host_taxID' + #if str($adv.enzyme_taxIDs) != "": + --enzyme_taxIDs '$adv.enzyme_taxIDs' + #end if --nb_ids '$adv.nb_ids' --to_csv '$uniprot_ids_csv' ]]></command> <inputs> - <param name="pathway" type="data" format="xml" label="Pathway (SBML)" /> + <param name="pathway" type="data" format="xml" label="Pathway (SBML)" /> <section name="adv" title="Advanced Options" expanded="false"> - <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" /> - <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" /> - <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" /> - <param name="NoMSA" type="boolean" label="Do not compute MSA/conservation scores ?" checked="true" display="checkboxes" /> - <param name="taxonIDs" type="text" label="Comma separated taxon ids (first considered as the host)" value="83333" /> + <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" /> + <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" /> + <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" /> + <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" /> + <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" /> + <param name="NoMSA" type="boolean" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" /> </section> </inputs> <outputs> @@ -50,7 +57,8 @@ * **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)] * **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)] * **NoMSA**\ : (boolean) Do not compute MSA/conservation scores -* **taxonIDs**\ : (string) Comma separated taxon ids [default: 83333 (E. coli K12)]. The first taxon ID is the one of the chassis, following ones are taxon IDs of output enzyme sequences +* **host_taxID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12]) +* **enzyme_taxIDs**\ : (string) Comma separated taxon IDs of output enzyme sequences Output ------ @@ -65,7 +73,7 @@ Version ---------- -0.1.0 +0.2.0 Authors ------- @@ -83,16 +91,6 @@ ]]></help> <citations> - <citation type="bibtex"> -@article{10.1093/bioinformatics/bty065, - title={Selenzyme: enzyme selection tool for pathway design}, - author={Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J Turner, Nigel S Scrutton, Douglas B Kell, Rainer Breitling, Jean-Loup Faulon}, - volume={34}, - pages={2153–2154}, - year={2018}, - doi = {10.1093/bioinformatics/bty065}, - url = {https://doi.org/10.1093/bioinformatics/bty065}, -} - </citation> + <citation type="doi">10.1093/bioinformatics/bty065</citation> </citations> </tool> \ No newline at end of file