# HG changeset patch
# User youngkim
# Date 1459358927 14400
# Node ID 161866cee2a2ecd675f53858e042c6512404c812
# Parent 736260d32237d0ee73ea0abd1041b982f9054a76
wrapper rename
diff -r 736260d32237 -r 161866cee2a2 BAMqc.xml
--- a/BAMqc.xml Wed Mar 30 13:06:41 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
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- perform QC on BAM files of NGS dataset
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- BAMqc
- samtools
- R
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- BAMqc.sh
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- -r '${refdb}'
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- -f '${attrID}'
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- -R '${rRNAdb}'
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- -s '$stranded'
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- -o "$output"
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- #set $core = len($files)
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- -p $core
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- #if str($cond_adv_options.adv_options) == 'yes':
- -q '$cond_adv_options.mapq'
- #end if
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- #for $file in $files
- '$file.input'
- '$file.input.tag'
- #end for
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-**What it does**
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-This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample.
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------
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-The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
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-ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
-
-.. _CSHL: `Cold Spring Harbor Laboratory`_
-.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
-.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
-.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
-.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
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diff -r 736260d32237 -r 161866cee2a2 ezBAMQC.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC.xml Wed Mar 30 13:28:47 2016 -0400
@@ -0,0 +1,108 @@
+
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+ perform QC on BAM files of NGS dataset
+
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+ ezBAMQC
+ R
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+
+
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+ ezBAMQC.sh
+
+ -r '${refdb}'
+
+ -f '${attrID}'
+
+ -R '${rRNAdb}'
+
+ -s '$stranded'
+
+ -o "$output"
+
+ #set $core = len($files)
+
+ -p $core
+
+ #if str($cond_adv_options.adv_options) == 'yes':
+ -q '$cond_adv_options.mapq'
+ #end if
+
+ #for $file in $files
+ '$file.input'
+ '$file.input.tag'
+ #end for
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+**What it does**
+
+This tool takes the mapping results from NGS libraries (BAM), and performs rapid quality assessment. If multiple files are provided, it will calculate and display correlation between each sample.
+
+-----
+
+The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
+
+ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
+
+.. _CSHL: `Cold Spring Harbor Laboratory`_
+.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
+.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
+.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
+.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
+
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