Mercurial > repos > yating-l > jbrowsearchivecreator
diff jbrowseArchiveCreator.xml @ 14:3f9971a91096 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
| author | yating-l |
|---|---|
| date | Wed, 20 Jun 2018 17:24:45 -0400 |
| parents | 43a700afd457 |
| children | 6464399df918 |
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--- a/jbrowseArchiveCreator.xml Tue Jun 19 17:59:51 2018 -0400 +++ b/jbrowseArchiveCreator.xml Wed Jun 20 17:24:45 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.2.1"> +<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.0"> <description> This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin </description> @@ -108,20 +108,21 @@ $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" - ##set database = str($f.formatChoice.bedChoice.database) - ##silent $extra_data_dict.update({"database": $database}) + #set database = str($f.formatChoice.bedChoice.database) + #silent $extra_data_dict.update({"database": $database}) #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" - ##set database = str($f.formatChoice.bedChoice.database) - ##silent $extra_data_dict.update({"database": $database}) + #set database = str($f.formatChoice.bedChoice.database) + #silent $extra_data_dict.update({"database": $database}) #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, $extra_data_dict) #end if #end if #if $f.formatChoice.format_select == "blastxml" - #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) + #set database = str($f.formatChoice.database) + #silent $extra_data_dict.update({"database": $database, "nameIndex": str($f.formatChoice.nameIndex)}) #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final, extra_data_dict) #end if @@ -251,6 +252,12 @@ type="data" label="Bed Blast Alignments (Bed12+12) File" /> + <param name="database" type="select" label="Protein database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="UniProt">UniProt</option> + <option value="FlyBase">FlyBase</option> + <option value="Others">Others</option> + </param> <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed_blat_alignment_option"> @@ -260,6 +267,10 @@ type="data" label="Bed BLAT Alignments (bigPsl) File" /> + <param name="database" type="select" label="mRNA database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="Others">Others</option> + </param> <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> </conditional> @@ -279,6 +290,12 @@ type="data" label="Blast Alignments File" /> + <param name="database" type="select" label="Protein database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="UniProt">UniProt</option> + <option value="FlyBase">FlyBase</option> + <option value="Others">Others</option> + </param> <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer>