details: http://www.bx.psu.edu/hg/galaxy/rev/b2a9827178e2 changeset: 1519:b2a9827178e2 user: Dan Blankenberg <dan(a)bx.psu.edu&gt; date: Fri Sep 19 12:27:20 2008 -0400 description: Update GMAJ tool interface. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (117 lines): diff -r 0f735b21dc12 -r b2a9827178e2 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Thu Sep 18 16:48:29 2008 -0400 +++ b/tools/visualization/GMAJ.xml Fri Sep 19 12:27:20 2008 -0400 @@ -3,7 +3,10 @@ <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."/> + <param name="refseq" label="Reference Sequence" type="select"> + <option value="first" selected="true">First sequence in each block</option> + <option value="any">Any sequence</option> + </param> <repeat name="annotations" title="Annotations"> <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'."> @@ -11,7 +14,7 @@ <option value="basic">Basic</option> </param> <when value="galaxy"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> + <param name="species" type="select" label="Species" multiple="False"> <options> <filter type="data_meta" ref="maf_input" key="species" /> </options> @@ -21,7 +24,6 @@ <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"> @@ -44,6 +46,7 @@ <option name="Skipping unsupported paragraph (maf_paragraph)" value="maf_paragraph"/> <option name="Skipping all reconstruction scores: no species specified (recon_noseq)" value="recon_noseq"/> <option name="Skipping reconstruction scores in blocks with missing row (recon_missing)" value="recon_missing"/> + <option name="The first row in some blocks is not the specified reference sequence (refseq_not_first)" value="refseq_not_first"/> <option name="Skipping extra MAF File (unused_maf)" value="unused_maf"/> </option> <option name="Annotation Files" value="annotations"> @@ -71,12 +74,15 @@ </option> <option name="Red Flags" value="red"> <option name="Sequence name in annotation file does not match name in MAF (seqname_mismatch)" value="seqname_mismatch"/> - <option name="BED Start or end &lt; 0 (bed_coord)" value="bed_coord"/> - <option name="GFF Start or end &lt; 1 (gff_coord)" value="gff_coord"/> + <option name="BED start or end &lt; 0 (bed_coord)" value="bed_coord"/> + <option name="GFF start or end &lt; 1 (gff_coord)" value="gff_coord"/> <option name="Missing item name for URL substitution (url_subst)" value="url_subst"/> </option> </option> <option name="Miscellaneous" value="miscellaneous"> + <option name="No refseq specified; assuming 'first' (default_refseq)" value="default_refseq"/> + <option name="One or more bundle entries are not used in parameters file(unused_entry)" value="unused_entry"/> + <option name="Skipping blocks for export where reference sequence is hidden or all gaps (export_skip)" value="export_skip"/> <option name="Possible parse error: token ends with an escaped quote (escaped_quote)" value="escaped_quote"/> <option name="Draggable panel dividers will not be sticky (no_sticky)" value="no_sticky"/> </option> @@ -89,11 +95,7 @@ title = "Galaxy: $maf_input.name" alignfile = input.maf -#if $refseq.value: refseq = $refseq -#else: -refseq = any -#end if tabext = .bed .gff .gtf #if $nowarn.value: nowarn = $nowarn @@ -102,36 +104,35 @@ #set $seq_count = 0 #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]] +#if $maf_input.dataset.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.dataset.metadata.species_chromosomes and $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] #else: #set $seq_names = [$annotation.annotation_style['species']] -#set $aliases = [""] #end if #else: #set $seq_names = [$annotation.annotation_style['seq_name']] -#set $aliases = [""] #end if -#for $seq_name, $alias in $zip( $seq_names, $aliases ): +#for $seq_name in $seq_names: seq ${seq_count}: seqname = $seq_name #if $annotation.annotation_style['exons_file'].dataset: -exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if #if $annotation.annotation_style['repeats_file'].dataset: -repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if #if $annotation.annotation_style['links_file'].dataset: -links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if #if $annotation.annotation_style['underlays_file'].dataset: -underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if #if $annotation.annotation_style['highlights_file'].dataset: -highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if +#if $annotation.annotation_style.style == "basic": offset = $annotation.annotation_style['offset'] +#end if #set $seq_count = $seq_count + 1 #end for