Mercurial > repos > iuc > jbrowse
diff jbrowse.xml @ 4:67b69bf76cd5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 129cbeb898c437fbf271f306cd57397204b034e1
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 16:02:37 -0400 |
| parents | 3b7938dfd6f9 |
| children | b55fad376d87 |
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--- a/jbrowse.xml Mon May 04 14:04:09 2015 -0400 +++ b/jbrowse.xml Mon May 04 16:02:37 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse" name="JBrowse" version="1.0"> +<tool id="jbrowse" name="JBrowse" version="0.1"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -9,13 +9,13 @@ <command interpreter="python"><![CDATA[jbrowse.py $positional_1 -#set repeat_var_2 = '" "'.join([ str($var.gff3) for $var in $repeat_2 ]) -#set repeat_var_3 = '" "'.join([ str($var.gff3.ext) for $var in $repeat_2 ]) -#set repeat_var_4 = '" "'.join([ str($var.gff3_label) for $var in $repeat_2 ]) +#set data_files = '" "'.join([ str($var.gff3) for $var in $data_tracks ]) +#set data_formats = '" "'.join([ str($var.gff3.ext) for $var in $data_tracks ]) +#set data_labels = '" "'.join([ str($var.gff3_label) for $var in $data_tracks ]) ---gff3 "$repeat_var_2" ---gff3_format "$repeat_var_3" ---gff3_label "$repeat_var_4" +--gff3 "$data_files" +--gff3_format "$data_formats" +--gff3_label "$data_labels" --jbrowse \${JBROWSE_SOURCE_DIR} @@ -23,7 +23,7 @@ > $default]]></command> <inputs> <param label="Genome" name="positional_1" type="data" format="fasta"/> - <repeat name="repeat_2" title="Annotation Track"> + <repeat name="data_tracks" title="Annotation Track"> <param label="GFF3/BED" format="gff,gff3,bed" name="gff3" type="data"/> <param label="Dataset Label" name="gff3_label" type="text"/> @@ -35,5 +35,8 @@ <help><![CDATA[ Deploy a static JBrowse visualization of a genome and some associated datasets ]]></help> + <citations> + <citation type="doi">10.1101/gr.094607.109</citation> + </citations> </tool>