mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Merge with b2a9827178e28d93e2a978f64033a556a72b4c51
This commit is contained in:
Wen-Yu Chung
@@ -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 @@ nowarn = $nowarn
|
||||
#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
|
||||
|
||||
Reference in New Issue
Block a user