details: http://www.bx.psu.edu/hg/galaxy/rev/f9d00dbefdec changeset: 1499:f9d00dbefdec user: Dan Blankenberg dan@bx.psu.edu date: Mon Sep 08 16:00:49 2008 -0400 description: Update GMAJ tool to allow the specifying of annotations in two styles.
1 file(s) affected in this change:
tools/visualization/GMAJ.xml
diffs (144 lines):
diff -r ad69f789d1cd -r f9d00dbefdec tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Mon Sep 08 14:54:40 2008 -0400 +++ b/tools/visualization/GMAJ.xml Mon Sep 08 16:00:49 2008 -0400 @@ -1,21 +1,40 @@ -<tool id="gmaj_1" name="GMAJ" Version="2.0.0"> +<tool id="gmaj_1" name="GMAJ" Version="2.0.1"> <description>Multiple Alignment Viewer</description> <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> - <options> - <filter type="data_meta" ref="maf_input" key="species" /> - </options> - </param> - <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> - <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> - <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> - <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> - <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> - <param name="offset" label="Offset" value="0" type="integer"/> + <conditional name="annotation_style"> + <param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'."> + <option value="galaxy" selected="true">Galaxy</option> + <option value="basic">Basic</option> + </param> + <when value="galaxy"> + <param name="species" type="select" label="Species of Annotation" multiple="False"> + <options> + <filter type="data_meta" ref="maf_input" key="species" /> + </options> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + <when value="basic"> + <param name="seq_name" label="Full Sequence Name" value="" type="text"> + <validator type="empty_field" message="You must supply the sequence name"/> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + </conditional> </repeat> <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to Suppress" separator=" " help="These do not affect behavior, only suppress warning messages."> <options> @@ -81,52 +100,59 @@ #end if
#set $seq_count = 0 -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: -#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] -#else -#set $seq_names = [$annotation['species'].value] +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style.style == "galaxy": +#if $maf_input.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#else: +#set $seq_names = [$annotation.annotation_style['species']] +#set $aliases = [""] #end if -#for $seq_name in $seq_names: +#else: +#set $seq_names = [$annotation.annotation_style['seq_name']] +#set $aliases = [""] +#end if +#for $seq_name, $alias in $zip( $seq_names, $aliases ): seq ${seq_count}: seqname = $seq_name -#if $annotation['exons_file'].dataset: -exons = ${spec_count}.exons.${annotation['exons_file'].extension} +#if $annotation.annotation_style['exons_file'].dataset: +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias #end if -#if $annotation['repeats_file'].dataset: -repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias #end if -#if $annotation['links_file'].dataset: -links = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias #end if -#if $annotation['underlays_file'].dataset: -underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias #end if -#if $annotation['highlights_file'].dataset: -highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias #end if -offset = $annotation['offset'] +offset = $annotation.annotation_style['offset']
#set $seq_count = $seq_count + 1 #end for #end for </configfile> <configfile name="filenames_file"> -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['exons_file'].dataset: -$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension} +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style['exons_file'].dataset: +$annotation.annotation_style['exons_file'] = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if -#if $annotation['repeats_file'].dataset: -$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +$annotation.annotation_style['repeats_file'] = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if -#if $annotation['links_file'].dataset: -$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +$annotation.annotation_style['links_file'] = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if -#if $annotation['underlays_file'].dataset: -$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +$annotation.annotation_style['underlays_file'] = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if -#if $annotation['highlights_file'].dataset: -$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +$annotation.annotation_style['highlights_file'] = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if #end for </configfile>