| Previous changeset 1:8a51813206ac (2019-07-11) Next changeset 3:fe5b82d00d6d (2019-08-10) |
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Commit message:
change in parameter setup for upstream region |
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modified:
glassgo_wrapper.xml |
| b |
| diff -r 8a51813206ac -r 5528ee7c99f2 glassgo_wrapper.xml --- a/glassgo_wrapper.xml Thu Jul 11 17:27:06 2019 -0400 +++ b/glassgo_wrapper.xml Mon Jul 15 03:53:29 2019 -0400 |
| b |
| @@ -5,11 +5,17 @@ </requirements> <command> GLASSgo.py - -i $input + -i ${input_data.input} + -d ${input_data.database} #if str($search.cond_param_setup.param_setup) == "manual": -e ${search.cond_param_setup.evalue} -p ${search.cond_param_setup.identity} #end if + -u ${additional_setting.upstream_region} + #if str($search.cond_taxon_setup.taxon_setup) == "acclist": + -g ${search.cond_taxon_setup.acclist} + #end if + -o $output </command> <inputs> @@ -23,38 +29,15 @@ </param> </section> <section name="search" title="Search Parameters" expanded="true"> - <param name="taxon_selection" type="select" label="Taxon Selection"> - <option value="global">global</option> - <option value="alphaproteobacteria">Alphaproteobacteria</option> - <option value="acquificiae">Aquificiae</option> - <option value="archaea">Archaea</option> - <option value="armatimonadetes">Armatimonadetes</option> - <option value="bacteria">Bacteria</option> - <option value="bacteroidetes">Bacteroidetes</option> - <option value="caldiserica">Caldiserica</option> - <option value="chlamydiae">Chlamydiae</option> - <option value="chloroflexi">Chloroflexi</option> - <option value="chrysiogenetes">Chrysiogenetes</option> - <option value="cyanobacteria">Cyanobacteria</option> - <option value="deferribacteres">Deferribacteres</option> - <option value="deinococcus-thermus">Deinococcus-thermus</option> - <option value="dictyoglomi">Dictyoglomi</option> - <option value="elusimicrobia">Elusimicrobia</option> - <option value="fibrobacteres">Fibrobacteres</option> - <option value="firmicutes">Firmicutes</option> - <option value="fusobacteria">Fusobacteria</option> - <option value="gemmatimonadetes">Gemmatimonadetes</option> - <option value="nitrospinae">Nitrospinae</option> - <option value="nitrospirae">Nitrospirae</option> - <option value="planctomycetes">Planctomycetes</option> - <option value="proteobacteria">Proteobacteria</option> - <option value="spirochaetes">Spirochaetes</option> - <option value="synergistetes">Synergistetes</option> - <option value="tenericutes">Tenericutes</option> - <option value="thermodesulfobacteria">Thermodesulfobacteria</option> - <option value="thermotogae">Thermotogae</option> - <option value="viruses">Viruses</option> - </param> + <conditional name="cond_taxon_setup"> + <param name="taxon_setup" type="select" label="Taxon Selection"> + <option value="global">global search</option> + <option value="acc">accession list from user history</option> + </param> + <when value="acc"> + <param name="acclist" type="data" format="txt" label="Accession List"/> + </when> + </conditional> <conditional name="cond_param_setup"> <param name="param_setup" type="select" display="radio" label="Parameter Setup"> <option value="automatic">automatic</option> |