opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

MAF Filter tool now accepts comma separated lists of chromosomes.

Browse Source
This commit is contained in:
Daniel Blankenberg
2007-11-08 21:57:27 +00:00
parent 29c9521010
commit 446f677bdd
1 changed files with 17 additions and 17 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/filters/maf/maf_filter.xml
+17 -17
View File
@@ -39,8 +39,8 @@
</when>
<when value="attribute_chr">
<param name="species2_is_isnot" type="select" label="Conditional">
<option value="==">Is</option>
<option value="!=">Is Not</option>
<option value="in">Is</option>
<option value="not in">Is Not</option>
</param>
<param name="species2_attribute" type="text" label="Chromosome" value="chr1"/>
</when>
@@ -49,8 +49,8 @@
</when>
<when value="attribute_chr">
<param name="species1_is_isnot" type="select" label="Conditional">
<option value="==">Is</option>
<option value="!=">Is Not</option>
<option value="in">Is</option>
<option value="not in">Is Not</option>
</param>
<param name="species1_attribute" type="text" label="Chromosome" value="chr1"/>
<repeat name="filter_condition" title="Filter Condition">
@@ -72,8 +72,8 @@
</when>
<when value="attribute_chr">
<param name="species2_is_isnot" type="select" label="Conditional">
<option value="==">Is</option>
<option value="!=">Is Not</option>
<option value="in">Is</option>
<option value="not in">Is Not</option>
</param>
<param name="species2_attribute" type="text" label="Chromosome" value="chr1"/>
</when>
@@ -86,41 +86,41 @@
</inputs>
<configfiles>
<configfile name="maf_filter_file">
#set $is_isnot_valid = {"==":"==", "!=":"!="}
def maf_block_pass_filter(maf_block):
#set $is_isnot_valid = {"==":"==", "!=":"!=", "in":"in", "not in":"not in"}
def maf_block_pass_filter( maf_block ):
#for $maf_filter in $maf_filters:
#if $len($maf_filter['species1_attributes']['filter_condition']) == 0:
#if $len( $maf_filter['species1_attributes']['filter_condition'] ) == 0:
#continue
#end if
primary_component = maf_block.get_component_by_src_start("""$maf_filter['species1'].encode('string_escape')""".decode('string_escape'))
primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].encode( 'string_escape' )""".decode( 'string_escape' ) )
if primary_component is not None:
#if $maf_filter['species1_attributes']['species1_attribute_type'] == 'attribute_chr':
if primary_component.src.split(".")[-1] $is_isnot_valid.get($maf_filter['species1_attributes']['species1_is_isnot'].strip(), '==') """$maf_filter['species1_attributes']['species1_attribute'].encode('string_escape')""".decode('string_escape'):
if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ):
#else
if primary_component.strand $is_isnot_valid.get($maf_filter['species1_attributes']['species1_is_isnot'].strip(), '==') """$maf_filter['species1_attributes']['species1_attribute'].encode('string_escape')""".decode('string_escape'):
if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ):
#end if
#for $filter_condition in $maf_filter['species1_attributes']['filter_condition']:
secondary_component = maf_block.get_component_by_src_start("""$filter_condition['species2'].encode('string_escape')""".decode('string_escape'))
secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].encode( 'string_escape' )""".decode( 'string_escape' ) )
#if $filter_condition['species2_attributes']['species2_attribute_type'] == 'attribute_chr':
if secondary_component is not None:
if not (secondary_component.src.split(".")[-1] $is_isnot_valid.get($filter_condition['species2_attributes']['species2_is_isnot'].strip(), '==') """$filter_condition['species2_attributes']['species2_attribute'].encode('string_escape')""".decode('string_escape')):
if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ):
return False
#else:
if secondary_component is not None:
if not (secondary_component.strand $is_isnot_valid.get($filter_condition['species2_attributes']['species2_is_isnot'].strip(), '==') """$filter_condition['species2_attributes']['species2_attribute'].encode('string_escape')""".decode('string_escape')):
if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ) ):
return False
#end if
#end for
#end for
return True
ret_val = maf_block_pass_filter(maf_block)
ret_val = maf_block_pass_filter( maf_block )
</configfile>
</configfiles>
<outputs>
<data format="maf" name="out_file1" />
</outputs>
<help>
This tool allows you to build complex filters to be applied to each alignment block of a MAF file. You can define restraints on species based upon chromosome and strand.
This tool allows you to build complex filters to be applied to each alignment block of a MAF file. You can define restraints on species based upon chromosome and strand. You can specify comma separated lists of chromosomes where appropriate.
.. class:: infomark