details: http://www.bx.psu.edu/hg/galaxy/rev/d146ca99434f
changeset: 2850:d146ca99434f
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Thu Oct 08 11:33:43 2009 -0400
description:
Fixed ascending/descending bug on Sort, and added ability to specify ascending or descending on each column.
2 file(s) affected in this change:
tools/filters/sorter.py
tools/filters/sorter.xml
diffs (100 lines):
diff -r 674bb364697a -r d146ca99434f tools/filters/sorter.py
--- a/tools/filters/sorter.py Thu Oct 08 11:14:04 2009 -0400
+++ b/tools/filters/sorter.py Thu Oct 08 11:33:43 2009 -0400
@@ -26,19 +26,20 @@
try:
inputfile = options.input
outputfile = '-o %s' % options.out_file1
- order = ('', '-r')[options.order == 'DESC']
columns = [options.column]
styles = [('','n')[options.style == 'num']]
- col_styles = sys.argv[6:]
- if len(col_styles) > 1:
- columns.extend([col_styles[i] for i in range(0,len(col_styles),2)])
- styles.extend([('','n')[col_styles[i] == 'num'] for i in range(1,len(col_styles),2)])
- cols = [ '-k%s,%s%s'%(columns[i], columns[i], styles[i]) for i in range(len(columns)) ]
+ orders = [('','r')[options.order == 'DESC']]
+ col_style_orders = sys.argv[6:]
+ if len(col_style_orders) > 1:
+ columns.extend([col_style_orders[i] for i in range(0,len(col_style_orders),3)])
+ styles.extend([('','n')[col_style_orders[i] == 'num'] for i in range(1,len(col_style_orders),3)])
+ orders.extend([('','r')[col_style_orders[i] == 'DESC'] for i in range(2,len(col_style_orders),3)])
+ cols = [ '-k%s,%s%s%s'%(columns[i], columns[i], styles[i], orders[i]) for i in range(len(columns)) ]
except Exception, ex:
stop_err('Error parsing input parameters\n' + str(ex))
# Launch sort.
- cmd = "sort -f -t $'\t' %s %s %s %s" % (order, ' '.join(cols), outputfile, inputfile)
+ cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile)
try:
os.system(cmd)
except Exception, ex:
diff -r 674bb364697a -r d146ca99434f tools/filters/sorter.xml
--- a/tools/filters/sorter.xml Thu Oct 08 11:14:04 2009 -0400
+++ b/tools/filters/sorter.xml Thu Oct 08 11:33:43 2009 -0400
@@ -10,6 +10,7 @@
#for $col in $column_set:
${col.other_column}
${col.other_style}
+ ${col.other_order}
#end for
</command>
<inputs>
@@ -19,17 +20,21 @@
<option value="num">Numerical sort</option>
<option value="alpha">Alphabetical sort</option>
</param>
+ <param name="order" type="select" label="everything in">
+ <option value="DESC">Descending order</option>
+ <option value="ASC">Ascending order</option>
+ </param>
<repeat name="column_set" title="Column selection">
<param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" />
<param name="other_style" type="select" label="with flavor">
<option value="num">Numerical sort</option>
<option value="alpha">Alphabetical sort</option>
</param>
+ <param name="other_order" type="select" label="everything in">
+ <option value="DESC">Descending order</option>
+ <option value="ASC">Ascending order</option>
+ </param>
</repeat>
- <param name="order" type="select" label="everything in">
- <option value="DESC">Descending order</option>
- <option value="ASC">Ascending order</option>
- </param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
@@ -39,18 +44,20 @@
<param name="input" value="sort_in1.bed"/>
<param name="column" value="1"/>
<param name="style" value="num"/>
+ <param name="order" value="ASC"/>
<param name="other_column" value="3"/>
<param name="other_style" value="num"/>
- <param name="order" value="ASC"/>
+ <param name="other_order" value="ASC"/>
<output name="out_file1" file="sort_out1.bed"/>
</test>
<test>
<param name="input" value="sort_in1.bed"/>
<param name="column" value="3"/>
<param name="style" value="alpha"/>
+ <param name="order" value="ASC"/>
<param name="other_column" value="1"/>
<param name="other_style" value="alpha"/>
- <param name="order" value="ASC"/>
+ <param name="other_order" value="ASC"/>
<output name="out_file1" file="sort_out2.bed"/>
</test>
</tests>
@@ -64,7 +71,7 @@
**Syntax**
-This tool sorts the dataset on any number of columns in either ascending or descending order (all columns will be ascending or descending).
+This tool sorts the dataset on any number of columns in either ascending or descending order.
* Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify.
* Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2).
details: http://www.bx.psu.edu/hg/galaxy/rev/c8ba2a78e696
changeset: 2851:c8ba2a78e696
user: Anton Nekrutenko <anton(a)bx.psu.edu>
date: Thu Oct 08 13:33:54 2009 -0400
description:
More interface updates
2 file(s) affected in this change:
tools/sr_mapping/bowtie_wrapper.xml
tools/sr_mapping/bwa_wrapper.xml
diffs (46 lines):
diff -r d146ca99434f -r c8ba2a78e696 tools/sr_mapping/bowtie_wrapper.xml
--- a/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 11:33:43 2009 -0400
+++ b/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 13:33:54 2009 -0400
@@ -426,9 +426,19 @@
**What it does**
-Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. Reads can be as long as 1024 base pairs, though shorter is better. Bowtie produces a specific output format which is converted to SAM by this tool.
+Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell.
.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
+
+------
+
+**Know what you are doing**
+
+.. class:: warningmark
+
+There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy.
+
+ .. __: http://bowtie-bio.sourceforge.net/index.shtml
------
diff -r d146ca99434f -r c8ba2a78e696 tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 11:33:43 2009 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 13:33:54 2009 -0400
@@ -291,7 +291,17 @@
**What it does**
-**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm and is aimed towards short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori.
+BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute.
+
+------
+
+**Know what you are doing**
+
+.. class:: warningmark
+
+There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy.
+
+ .. __: http://bio-bwa.sourceforge.net/
------
details: http://www.bx.psu.edu/hg/galaxy/rev/ebe3e881ac25
changeset: 2843:ebe3e881ac25
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Wed Oct 07 15:31:18 2009 -0400
description:
Updated several sample index loc files to make it clearer how the actual loc files should appear
4 file(s) affected in this change:
tool-data/bowtie_indices.loc.sample
tool-data/sam_fa_indices.loc.sample
tool-data/sequence_index_base.loc.sample
tool-data/sequence_index_color.loc.sample
diffs (89 lines):
diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/bowtie_indices.loc.sample
--- a/tool-data/bowtie_indices.loc.sample Wed Oct 07 15:25:16 2009 -0400
+++ b/tool-data/bowtie_indices.loc.sample Wed Oct 07 15:31:18 2009 -0400
@@ -1,8 +1,8 @@
#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Bowtie indexed sequences data files. You will need
#to create these data files and then create a bowtie_indices.loc file
-#similar to this one (store it in this directory ) that points to
-#the directories in which those files are stored. The bowtie_indices.loc
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
#file has this format (white space characters are TAB characters):
#
#<build> <file_base>
@@ -26,3 +26,4 @@
#exist, but it is the prefix for the actual index files. For example:
#
#hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#hg19 /depot/data2/galaxy/bowtie/hg19/hg19
diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sam_fa_indices.loc.sample
--- a/tool-data/sam_fa_indices.loc.sample Wed Oct 07 15:25:16 2009 -0400
+++ b/tool-data/sam_fa_indices.loc.sample Wed Oct 07 15:31:18 2009 -0400
@@ -1,17 +1,17 @@
#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Samtools indexed sequences data files. You will need
#to create these data files and then create a sam_fa_indices.loc file
-#similar to this one (store it in this directory ) that points to
-#the directories in which those files are stored. The sam_fa_indices.loc
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The sam_fa_indices.loc
#file has this format (white space characters are TAB characters):
#
-#<index> <seq> <location>
+#index <seq> <location>
#
#So, for example, if you had hg18 indexed stored in
#/depot/data2/galaxy/sam/,
#then the sam_fa_indices.loc entry would look like this:
#
-#hg18 /depot/data2/galaxy/sam/hg18.fa
+#index hg18 /depot/data2/galaxy/sam/hg18.fa
#
#and your /depot/data2/galaxy/sam/ directory
#would contain hg18.fa and hg18.fa.fai files:
@@ -24,4 +24,5 @@
#exist, but it should never be directly used. Instead, the name serves
#as a prefix for the index file. For example:
#
-#hg18 /depot/data2/galaxy/sam/hg18.fa
+#index hg18 /depot/data2/galaxy/sam/hg18.fa
+#index hg19 /depot/data2/galaxy/sam/hg19.fa
diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sequence_index_base.loc.sample
--- a/tool-data/sequence_index_base.loc.sample Wed Oct 07 15:25:16 2009 -0400
+++ b/tool-data/sequence_index_base.loc.sample Wed Oct 07 15:31:18 2009 -0400
@@ -1,8 +1,8 @@
#This is a sample file distributed with Galaxy that enables tools
#to use a directory of BWA indexed sequences data files. You will need
#to create these data files and then create a sequence_index_base.loc file
-#similar to this one (store it in this directory ) that points to
-#the directories in which those files are stored. The sequence_index_base.loc
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The sequence_index_base.loc
#file has this format (white space characters are TAB characters):
#
#<build> <file_base>
@@ -26,3 +26,4 @@
#exist, but it is the prefix for the actual index files. For example:
#
#phiX /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18 /depot/data2/galaxy/hg18/base/hg18.fa
diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sequence_index_color.loc.sample
--- a/tool-data/sequence_index_color.loc.sample Wed Oct 07 15:25:16 2009 -0400
+++ b/tool-data/sequence_index_color.loc.sample Wed Oct 07 15:31:18 2009 -0400
@@ -1,8 +1,8 @@
#This is a sample file distributed with Galaxy that enables tools
#to use a directory of BWA indexed sequences data files. You will need
#to create these data files and then create a sequence_index_color.loc file
-#similar to this one (store it in this directory ) that points to
-#the directories in which those files are stored. The sequence_index_color.loc
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The sequence_index_color.loc
#file has this format (white space characters are TAB characters):
#
#<build> <file_base>
@@ -26,3 +26,4 @@
#exist, but it is the prefix for the actual index files. For example:
#
#phiX /depot/data2/galaxy/phiX/color/phiX.fa
+#hg18 /depot/data2/galaxy/hg18/color/hg18.fa