details:
http://www.bx.psu.edu/hg/galaxy/rev/b2a9827178e2
changeset: 1519:b2a9827178e2
user: Dan Blankenberg <dan(a)bx.psu.edu>
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 < 0 (bed_coord)"
value="bed_coord"/>
- <option name="GFF Start or end < 1 (gff_coord)"
value="gff_coord"/>
+ <option name="BED start or end < 0 (bed_coord)"
value="bed_coord"/>
+ <option name="GFF start or end < 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