galaxy-dist commit 4ee5fca864a4: lims: find samples
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1283367408 14400
# Node ID 4ee5fca864a44b2bf7e7efac7a97f564961df3f2
# Parent f41f4ace420a58e7316fbeddacd301ff6d5dfaf1
lims: find samples
- the search settings are saved after the search
- search now case insensitive and wildcard support added
- masthead problem fixed when showing find samples page in user mode
--- a/templates/requests/common/find.mako
+++ b/templates/requests/common/find.mako
@@ -54,47 +54,60 @@
<div class="toolFormBody"><form name="find_request" id="find_request" action="${h.url_for( controller='requests_common', action='find', cntrller=cntrller)}" method="post" ><div class="form-row">
- <label>Find in sequencing requests in state:</label>
- <select name="request_state">
- <option value="In Progress" selected>In-Progress</option>
- <option value="Complete">Complete</option>
- <option value="Both">Both</option>
- </select>
+ <label>Find sample(s) using:</label>
+ ${search_type.get_html()}
+ <div class="toolParamHelp" style="clear: both;">
+ Select a sample attribute to search through all the samples.<br/>
+ To search for a sample with a dataset name, select the dataset
+ option above. This will return all the sample(s) which has a
+ dataset with the given name associated with it. To search for
+ all samples created on a certain date select the 'date created'
+ option above. Enter date in 'YYYY-MM-DD' format.
+ </div></div><div class="form-row">
- <label>Find by sample:</label>
- <select name="search_type">
- <option value="name" selected>name</option>
- <option value="bar_code">barcode</option>
- </select>
+ <label>Filter sequencing requests in state:</label>
+ ${request_states.get_html()}
+ <div class="toolParamHelp" style="clear: both;">
+ This will filter the search results to show only those sample(s) <br/>
+ whose parent sequencing request is in the selected state.
+ </div></div><div class="form-row">
- <input type="text" name="search_string" size="40" value="">
- <input type="submit" name="go_button" value="Go"/>
+ ${search_box.get_html()}
+ <input type="submit" name="go_button" value="Find"/>
+ <div class="toolParamHelp" style="clear: both;">
+ Wildcard search (%) can be used as placeholder for any sequence of characters or words.<br/>
+ For example, to search for samples starting with 'mysample' use 'mysample%' as the search string.
+ </div></div>
%if results:
<div class="form-row"><label><i>${results}</i></label>
+ <div class="toolParamHelp" style="clear: both;">
+ The search results are sorted by the date the samples where created.
+ </div></div>
%endif
<div class="form-row">
%if samples:
%for s in samples:
<div class="form-row">
- <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}"><label>Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</label></a>
+
+ Sample: ${s.name} | Barcode: ${s.bar_code}<br/>
+ State: ${s.current_state().name}<br/>
+ Datasets: <a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(s.id))}">${s.transferred_dataset_files()}/${len(s.datasets)}</a><br/>
%if cntrller == 'requests_admin':
<i>User: ${s.request.user.email}</i>
%endif
- <div class="toolParamHelp" style="clear: both;">
- Sample: ${s.name}<br/>
- Barcode: ${s.bar_code}<br/>
- State: ${s.current_state().name}
- </div>
+ <div class="toolParamHelp" style="clear: both;">
+ <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}">Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</a>
+ </div>
+
</div><br/>
%endfor
%endif
-
</div></form></div>
--- /dev/null
+++ b/templates/requests/find_index.mako
@@ -0,0 +1,16 @@
+<%inherit file="/webapps/galaxy/base_panels.mako"/>
+
+<%def name="init()">
+<%
+ self.has_left_panel=False
+ self.has_right_panel=False
+ self.active_view="requests"
+ self.message_box_visible=False
+%>
+</%def>
+
+<%def name="center_panel()">
+
+ <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="requests_common", action="find" )}"></iframe>
+
+</%def>
--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -135,6 +135,11 @@ class Requests( BaseController ):
@web.require_login( "create/submit sequencing requests" )
def index( self, trans ):
return trans.fill_template( "requests/index.mako" )
+
+ @web.expose
+ @web.require_login( "create/submit sequencing requests" )
+ def find_index( self, trans ):
+ return trans.fill_template( "requests/find_index.mako" )
@web.expose
@web.require_login( "create/submit sequencing requests" )
--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -1256,6 +1256,25 @@ class RequestsCommon( BaseController, Us
#
# Find sequencing requests & samples
#
+ def __find_widgets(self, trans, **kwd):
+ params = util.Params( kwd )
+ request_states = SelectField('request_states', multiple=True, display="checkboxes")
+ sel_op = kwd.get('request_states', trans.app.model.Request.states.SUBMITTED)
+ for i, s in trans.app.model.Request.states.items():
+ if s in sel_op:
+ request_states.add_option(s, s, True)
+ else:
+ request_states.add_option(s, s)
+ search_type = SelectField('search_type')
+ sel_op = kwd.get('search_type', 'sample name')
+ for s in ['sample name', 'barcode', 'dataset']:
+ if s in sel_op:
+ search_type.add_option(s, s, True)
+ else:
+ search_type.add_option(s, s)
+ search_box = TextField('search_box', 50, kwd.get('search_box', ''))
+ return request_states, search_type, search_box
+
@web.expose
@web.require_admin
def find( self, trans, **kwd ):
@@ -1263,26 +1282,31 @@ class RequestsCommon( BaseController, Us
cntrller = params.get( 'cntrller', 'requests' )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- search_string = kwd.get( 'search_string', '' )
- search_type = params.get( 'search_type', '' )
- if params.get( 'request_state', 'In Progress' ) == 'Both':
- request_states = ['In Progress', 'Complete']
- else:
- request_states = [params.get( 'request_state', 'In Progress' )]
-
-
samples_list = []
results = ''
- if params.get('go_button', '') == 'Go':
- if search_type == 'bar_code':
+ if params.get('go_button', '') == 'Find':
+ search_string = kwd.get( 'search_box', '' )
+ search_type = params.get( 'search_type', '' )
+ request_states = params.get( 'request_states', '' )
+ samples = []
+ if search_type == 'barcode':
samples = trans.sa_session.query( trans.app.model.Sample ) \
.filter( and_( trans.app.model.Sample.table.c.deleted==False,
trans.app.model.Sample.table.c.bar_code.like(search_string) ) )\
+ .order_by( trans.app.model.Sample.table.c.create_time.desc())\
.all()
- elif search_type == 'name':
+ elif search_type == 'sample name':
samples = trans.sa_session.query( trans.app.model.Sample ) \
.filter( and_( trans.app.model.Sample.table.c.deleted==False,
- trans.app.model.Sample.table.c.name.like(search_string) ) )\
+ trans.app.model.Sample.table.c.name.ilike(search_string) ) )\
+ .order_by( trans.app.model.Sample.table.c.create_time.desc())\
+ .all()
+ elif search_type == 'dataset':
+ samples = trans.sa_session.query( trans.app.model.Sample ) \
+ .filter( and_( trans.app.model.Sample.table.c.deleted==False,
+ trans.app.model.SampleDataset.table.c.sample_id==trans.app.model.Sample.table.c.id,
+ trans.app.model.SampleDataset.table.c.name.ilike(search_string) ) )\
+ .order_by( trans.app.model.Sample.table.c.create_time.desc())\
.all()
if cntrller == 'requests':
for s in samples:
@@ -1295,11 +1319,12 @@ class RequestsCommon( BaseController, Us
if not s.request.deleted \
and s.request.state() in request_states:
samples_list.append(s)
- results = 'There are %i sequencing requests matching the search parameters.' % len(samples_list)
+ results = 'There are %i sample(s) matching the search parameters.' % len(samples_list)
+ request_states, search_type, search_box = self.__find_widgets(trans, **kwd)
return trans.fill_template( '/requests/common/find.mako',
- cntrller=cntrller,
- samples=samples_list,
- results=results )
+ cntrller=cntrller, request_states=request_states,
+ samples=samples_list, search_type=search_type,
+ results=results, search_box=search_box )
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -82,7 +82,7 @@
<%
menu_options = [
[ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ],
- [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ],
+ [ 'Find Samples', h.url_for( controller='/requests', action='find_index' ) ],
[ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ]
]
tab( "lab", "Lab", None, menu_options=menu_options )
11 years, 8 months
galaxy-dist commit eb75925d4b97: lims: find samples
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1283369397 14400
# Node ID eb75925d4b9705ab8722cab41c321bf15a4b2359
# Parent e37392b073d89af5aea5e6206e9827ea6ad3f190
lims: find samples
- bug fix: filtering results by only one state is working
- UI improvements
--- a/templates/requests/common/find.mako
+++ b/templates/requests/common/find.mako
@@ -83,18 +83,19 @@
</div>
%if results:
<div class="form-row">
- <label><i>${results}</i></label>
- <div class="toolParamHelp" style="clear: both;">
- The search results are sorted by the date the samples where created.
- </div>
+ <label><i>${results}</i></label>
+ %if samples:
+ <div class="toolParamHelp" style="clear: both;">
+ The search results are sorted by the date the samples where created.
+ </div>
+ %endif
</div>
%endif
<div class="form-row">
%if samples:
%for s in samples:
<div class="form-row">
-
- Sample: ${s.name} | Barcode: ${s.bar_code}<br/>
+ Sample: <b>${s.name}</b> | Barcode: ${s.bar_code}<br/>
State: ${s.current_state().name}<br/>
Datasets: <a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(s.id))}">${s.transferred_dataset_files()}/${len(s.datasets)}</a><br/>
%if cntrller == 'requests_admin':
@@ -103,7 +104,6 @@
<div class="toolParamHelp" style="clear: both;"><a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}">Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</a></div>
-
</div><br/>
%endfor
--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -1287,7 +1287,7 @@ class RequestsCommon( BaseController, Us
if params.get('go_button', '') == 'Find':
search_string = kwd.get( 'search_box', '' )
search_type = params.get( 'search_type', '' )
- request_states = params.get( 'request_states', '' )
+ request_states = util.listify( params.get( 'request_states', '' ) )
samples = []
if search_type == 'barcode':
samples = trans.sa_session.query( trans.app.model.Sample ) \
11 years, 8 months
galaxy-dist commit 2ba0fe1297a8: lims : UI improvements to the request info page
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1283372432 14400
# Node ID 2ba0fe1297a8a31f99c412f05046ec7c2f749798
# Parent 12c032ebc303060b838448ad8f6e0da96cacb631
lims : UI improvements to the request info page
--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -1138,17 +1138,6 @@ class RequestsCommon( BaseController, Us
request = trans.sa_session.query( trans.app.model.Request ).get( id )
# list of widgets to be rendered on the request form
request_details = []
- # main details
- request_details.append(dict(label='Description',
- value=request.desc,
- helptext=''))
- request_details.append(dict(label='Date created',
- value=request.create_time,
- helptext=''))
- request_details.append(dict(label='Date updated',
- value=request.update_time,
- helptext=''))
-
# form fields
for index, field in enumerate(request.type.request_form.fields):
if field['required']:
--- a/templates/requests/common/show_request.mako
+++ b/templates/requests/common/show_request.mako
@@ -225,6 +225,15 @@ function showContent(vThis)
<tbody><tr><td valign="top" width="50%">
+ <div class="form-row">
+ <label>Description:</label>
+ %if request.desc:
+ ${request.desc}
+ %else:
+ <i>None</i>
+ %endif
+ </div>
+ <div style="clear: both"></div>
%for index, rd in enumerate(request_details):
<div class="form-row"><label>${rd['label']}:</label>
@@ -242,6 +251,14 @@ function showContent(vThis)
%endfor
</td><td valign="top" width="50%">
+ <div class="form-row">
+ <label>Date created:</label>
+ ${request.create_time}
+ </div>
+ <div class="form-row">
+ <label>Date updated:</label>
+ ${request.update_time}
+ </div><div class="form-row"><label>Email notification recipient(s):</label><% emails = ', '.join(request.notification['email']) %>
11 years, 8 months
galaxy-dist commit f41f4ace420a: For UI tab generation, only create link if there is an href.
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1283364901 14400
# Node ID f41f4ace420a58e7316fbeddacd301ff6d5dfaf1
# Parent 5f87abcf4854c6e5603a5b937865d3e8bdc9190d
For UI tab generation, only create link if there is an href.
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -26,7 +26,12 @@
if not visible:
style = "display: none;"
%>
- <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a>
+ <td class="${cls}" style="${style}">
+ %if href:
+ <a target="${target}" href="${href}">${display}</a>
+ %else:
+ ${display}
+ %endif
%if menu_options:
<div class="submenu"><ul>
11 years, 8 months
galaxy-dist commit 397241b761ab: Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b .
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User jeremy goecks <jeremy.goecks(a)emory.edu>
# Date 1283346658 14400
# Node ID 397241b761abe9a0cdad1f815e0a83328e3a665c
# Parent c79aa66e7fd2b69c73a1937a0a58aec2f98e06e2
Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b .
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -43,12 +43,12 @@
</test><!-- Test GFF file support. --><test>
- <param name="input" value="gff_filtering_out1.gff" dbkey="mm9" ftype="gff" />
+ <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out4.gff" /></test><test>
- <param name="input" value="gff_filtering_out1.gff" dbkey="mm9" ftype="gff" />
+ <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /><param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out5.fasta" /></test>
11 years, 8 months
galaxy-dist commit 37cbea4bf8c7: Added tool_conf.xml.main with BAM-to-SAM tool
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Kelly Vincent <kpvincent(a)bx.psu.edu>
# Date 1283350216 14400
# Node ID 37cbea4bf8c7995eea2b202fe3fcfbc72d0307a7
# Parent 09a684e9e0d42a3704e0093a15e54ad339da6329
Added tool_conf.xml.main with BAM-to-SAM tool
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -327,6 +327,7 @@
<tool file="samtools/sam_bitwise_flag_filter.xml" /><tool file="samtools/sam2interval.xml" /><tool file="samtools/sam_to_bam.xml" />
+ <tool file="samtools/bam_to_sam.xml" /><tool file="samtools/sam_merge.xml" /><tool file="samtools/sam_pileup.xml" /><tool file="samtools/pileup_parser.xml" />
11 years, 8 months
galaxy-dist commit 09a684e9e0d4: Added BAM-to-SAM tool
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Kelly Vincent <kpvincent(a)bx.psu.edu>
# Date 1283348652 14400
# Node ID 09a684e9e0d42a3704e0093a15e54ad339da6329
# Parent 397241b761abe9a0cdad1f815e0a83328e3a665c
Added BAM-to-SAM tool
--- /dev/null
+++ b/test-data/bam_to_sam_out1.sam
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
--- /dev/null
+++ b/tools/samtools/bam_to_sam.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+"""
+Converts BAM data to sorted SAM data.
+usage: bam_to_sam.py [options]
+ --input1: SAM file to be converted
+ --output1: output dataset in bam format
+"""
+
+import optparse, os, sys, subprocess, tempfile, shutil
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+#from galaxy import util
+
+def stop_err( msg ):
+ sys.stderr.write( '%s\n' % msg )
+ sys.exit()
+
+def __main__():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
+ parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
+ ( options, args ) = parser.parse_args()
+
+ tmp_dir = tempfile.mkdtemp()
+ try:
+ # exit if input file empty
+ if os.path.getsize( options.input1 ) == 0:
+ raise Exception, 'Initial BAM file empty'
+ # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ).
+ command = 'samtools view -o %s %s' % ( options.output1, options.input1 )
+ tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+ tmp_stderr = open( tmp, 'wb' )
+ proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
+ returncode = proc.wait()
+ tmp_stderr.close()
+ # get stderr, allowing for case where it's very large
+ tmp_stderr = open( tmp, 'rb' )
+ stderr = ''
+ buffsize = 1048576
+ try:
+ while True:
+ stderr += tmp_stderr.read( buffsize )
+ if not stderr or len( stderr ) % buffsize != 0:
+ break
+ except OverflowError:
+ pass
+ tmp_stderr.close()
+ if returncode != 0:
+ raise Exception, stderr
+ except Exception, e:
+ #clean up temp files
+ if os.path.exists( tmp_dir ):
+ shutil.rmtree( tmp_dir )
+ stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
+ #clean up temp files
+ if os.path.exists( tmp_dir ):
+ shutil.rmtree( tmp_dir )
+ # check that there are results in the output file
+ if os.path.getsize( options.output1 ) > 0:
+ sys.stdout.write( 'BAM file converted to SAM' )
+ else:
+ stop_err( 'The output file is empty, there may be an error with your input file.' )
+
+if __name__=="__main__": __main__()
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -286,6 +286,7 @@
<tool file="samtools/sam_bitwise_flag_filter.xml" /><tool file="samtools/sam2interval.xml" /><tool file="samtools/sam_to_bam.xml" />
+ <tool file="samtools/bam_to_sam.xml" /><tool file="samtools/sam_merge.xml" /><tool file="samtools/sam_pileup.xml" /><tool file="samtools/pileup_parser.xml" />
--- /dev/null
+++ b/tools/samtools/bam_to_sam.xml
@@ -0,0 +1,37 @@
+<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0">
+ <description>converts BAM format to SAM format</description>
+ <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command>
+ <inputs>
+ <param name="input1" type="data" format="bam" label="BAM File to Convert" />
+ </inputs>
+ <outputs>
+ <data name="output1" format="sam" />
+ </outputs>
+ <tests>
+ <test>
+ <!--
+ Bam-to-Sam command:
+ samtools view -o test-data/3.bam bam_to_sam_out1.sam
+ -->
+ <param name="input1" value="1.bam" ftype="bam" />
+ <output name="output1" file="bam_to_sam_out1.sam" />
+ </test>
+ <test>
+ <!--
+ Bam-to-Sam command:
+ samtools view -o test-data/1.sam bam_to_sam_out2.sam
+ -->
+ <param name="input1" value="3.bam" ftype="bam" />
+ <param name="output1" file="bam_to_sam_out2.sam" />
+ </test>
+ </tests>
+ <help>
+
+**What it does**
+
+This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
+
+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+
+ </help>
+</tool>
--- /dev/null
+++ b/test-data/bam_to_sam_out2.sam
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1095:605 0 chrM 23 25 36M * 0 0 AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1650:1185 0 chrM 14956 25 36M * 0 0 ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1483:1161 16 chrM 15080 25 36M * 0 0 TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1190:1283 16 chrM 15338 25 36M * 0 0 TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
11 years, 8 months
galaxy-dist commit 5f87abcf4854: fix for the menu item bug intriduced in changeset 4223:03d06d05bf62
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1283357789 14400
# Node ID 5f87abcf4854c6e5603a5b937865d3e8bdc9190d
# Parent 37cbea4bf8c7995eea2b202fe3fcfbc72d0307a7
fix for the menu item bug intriduced in changeset 4223:03d06d05bf62
now the Lab menu appears correctly for sample tracking users
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -74,18 +74,20 @@
## Lab menu.
%if trans.user and trans.user.accessible_request_types(trans):
- menu_options = [
- [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ],
- [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ],
- [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" )}, "galaxy_main" ],
- ]
- tab( "lab", "Lab", None, menu_options=menu_options )
+ <%
+ menu_options = [
+ [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ],
+ [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ],
+ [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ]
+ ]
+ tab( "lab", "Lab", None, menu_options=menu_options )
+ %>
%endif
## Visualization menu.
%if app.config.get_bool( 'enable_tracks', False ):
<%
- menu_options = [
+ menu_options = [
['New Track Browser', h.url_for( controller='/tracks', action='index' ) ],
['Saved Visualizations', h.url_for( controller='/visualization', action='list' ) ]
]
11 years, 8 months
galaxy-dist commit ce299d78b567: Tweaks to lines_diff in 2 rg tests to account for different versions of R and plink
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User fubar: ross Lazarus at gmail period com
# Date 1283301008 14400
# Node ID ce299d78b5670aa548b9ecad47754f6b5ce8584f
# Parent 03d06d05bf62a6444f1a652910708fde17fa189b
Tweaks to lines_diff in 2 rg tests to account for different versions of R and plink
--- a/tools/rgenetics/rgManQQ.xml
+++ b/tools/rgenetics/rgManQQ.xml
@@ -42,7 +42,7 @@
<param name='chrom_col' value='1' /><param name='offset_col' value='2' /><param name='grey' value='0' />
- <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='30'>
+ <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='40'><extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size"
delta = "10000"/><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size"
--- a/tools/rgenetics/rgQC.xml
+++ b/tools/rgenetics/rgQC.xml
@@ -32,8 +32,8 @@
<extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "5000"/><extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/><extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />
- <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" />
- <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" />
+ <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/>
+ <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/><extra_files type="file" name='tinywga.imendel' value="rgtestouts/rgQC/tinywga.imendel" compare="diff"/><extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" /><extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" />
11 years, 8 months
galaxy-dist commit c79aa66e7fd2: Another small tweak - no idea what combination of plink and other dependencies
by commits-noreply＠bitbucket.org
# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User fubar: ross Lazarus at gmail period com
# Date 1283313090 14400
# Node ID c79aa66e7fd2b69c73a1937a0a58aec2f98e06e2
# Parent ce299d78b5670aa548b9ecad47754f6b5ce8584f
Another small tweak - no idea what combination of plink and other dependencies
will have on lines_diff at other sites...but buildbot seems fussy
Still missing scipy and haploview seems unhappy too.
--- a/tools/rgenetics/rgQC.xml
+++ b/tools/rgenetics/rgQC.xml
@@ -30,7 +30,7 @@
<param name='out_prefix' value='rgQCtest1' /><output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='280'><extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "5000"/>
- <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/>
+ <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/><extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" /><extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/><extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/>
@@ -39,13 +39,13 @@
<extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" /><extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" /><extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="5000"/>
- <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" />
+ <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" lines_diff="10" /><extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="sim_size" delta="1000" /><extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" />
- <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="17"/>
+ <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="20"/><extra_files type="file" name='Ranked_Marker_HWE.xls' value="rgtestouts/rgQC/Ranked_Marker_HWE.xls" compare="diff" /><extra_files type="file" name='Ranked_Marker_MAF.xls' value="rgtestouts/rgQC/Ranked_Marker_MAF.xls" compare="diff" />
- <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" />
+ <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" lines_diff="5"/><extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="10"/><extra_files type="file" name='tinywga_fracmiss_cum.jpg' value="rgtestouts/rgQC/tinywga_fracmiss_cum.jpg" compare="sim_size" delta = "1000"/><extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "1000"/>
11 years, 8 months