Mercurial > repos > fubar > jbrowse2
diff macros.xml @ 93:4c517a0041a8 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
| author | fubar |
|---|---|
| date | Wed, 24 Apr 2024 02:29:32 +0000 |
| parents | 408781c080fc |
| children | 74074746ccd8 |
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--- a/macros.xml Sun Apr 21 04:42:29 2024 +0000 +++ b/macros.xml Wed Apr 24 02:29:32 2024 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.10.1</token> + <token name="@TOOL_VERSION@">2.11.0</token> <xml name = "edamInc"> <edam_topics> <edam_topic>topic_3307</edam_topic> @@ -20,7 +20,8 @@ <requirement type="package" version="6.0.1">pyyaml</requirement> <requirement type="package" version="1.11">tabix</requirement> <requirement type="package" version="4.6.0">findutils</requirement> - <requirement type="package" version="0.0.8">hictk</requirement> + <requirement type="package" version="0.0.12-0">hictk</requirement> + <requirement type="package" version="3.0">zip</requirement> <yield/> </requirements> </xml> @@ -539,51 +540,51 @@ <xml name="input_conditional" token_label="Track Data" token_format="data"> <conditional name="useuri"> - <param name="insource" type="select" label="Define track data as a history file or an internet URI" - help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> - <option value="history" selected="true">Track data from a history file</option> - <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> + <param name="insource" type="select" label="Define track data as a history file or an internet URI" + help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> + <option value="history" selected="true">Track data from a history file</option> + <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> + </param> + <when value="history"> + <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> + </when> + <when value="uri"> + <param label="@LABEL@" name="annouri" type="text" /> + <param label="Short name for track display" name="annoname" type="text" > + <sanitizer invalid_char="_"> + <valid initial="string.printable" > + <remove value="'" /> + </valid> + </sanitizer> </param> - <when value="history"> - <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> - </when> - <when value="uri"> - <param label="@LABEL@" name="annouri" type="text" /> - <param label="Short name for track display" name="annoname" type="text" > - <sanitizer invalid_char="_"> + </when> + </conditional> + </xml> + <xml name="pafref_conditional" token_label="Track Data" token_format="data"> + <conditional name="pafuseuri"> + <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" + help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> + <option value="history" selected="true">PAF reference comparison genome from a history file</option> + <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> + </param> + <when value="history"> + <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" + help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" /> + </when> + <when value="uri"> + <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> + <param label="@LABEL@" name="annotation" type="text" /> + <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space"> + <sanitizer invalid_char="_"> <valid initial="string.printable" > <remove value="'" /> </valid> - </sanitizer> - </param> - </when> - </conditional> - </xml> - <xml name="pafref_conditional" token_label="Track Data" token_format="data"> - <conditional name="pafuseuri"> - <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" - help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> - <option value="history" selected="true">PAF reference comparison genome from a history file</option> - <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> - </param> - <when value="history"> - <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" - help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" /> - </when> - <when value="uri"> - <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> - <param label="@LABEL@" name="annotation" type="text" /> - <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space"> - <sanitizer invalid_char="_"> - <valid initial="string.printable" > - <remove value="'" /> - </valid> - </sanitizer> - </param> - </repeat> - </when> - </conditional> - </xml> + </sanitizer> + </param> + </repeat> + </when> + </conditional> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-016-0924-1</citation>