# HG changeset patch
# User thanhlv
# Date 1551282849 18000
# Node ID f47f5ba2c9be4befdb500614e6d2b3c989f9da78
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 3ea7f0b0c83b2e404a61d5c50545fe4b3bd2d6c6-dirty
diff -r 000000000000 -r f47f5ba2c9be biotradis_add_tags.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_add_tags.xml Wed Feb 27 10:54:09 2019 -0500
@@ -0,0 +1,34 @@
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+ Generates a BAM file with tags added to read strings.
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+ macros.xml
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+ $log
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+ ]]>
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diff -r 000000000000 -r f47f5ba2c9be biotradis_bacteria_tradis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_bacteria_tradis.xml Wed Feb 27 10:54:09 2019 -0500
@@ -0,0 +1,96 @@
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+ Generates a BAM file with tags added to read strings.
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+ macros.xml
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+
+ > fq.list &&
+ #end for
+
+ bacteria_tradis -f fq.list
+ -t $tag
+ -r $ref
+ -td $tag_dir
+ -mm $mm
+ -m $m
+ #if str($smalt_k)!=""
+ --smalt_k $smalt_k
+ #end if
+ #if str($smalt_s)!=""
+ --smalt_s $smalt_s
+ #end if
+ --smalt_y $smalt_y
+ --smalt_r $smalt_r
+ -n "\${GALAXY_SLOTS:-2}"
+ #if $verbose
+ --verbose
+ #end if
+ && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
+ && tar cvzf mapped.tar.gz *mapped.bam*
+ ]]>
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+ >
+ >
+ >
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+ `_.
+ ]]>
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diff -r 000000000000 -r f47f5ba2c9be biotradis_check_tags.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_check_tags.xml Wed Feb 27 10:54:09 2019 -0500
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+ Check for the existence of tradis tags in a bam
+
+ macros.xml
+
+
+ $output
+
+ ]]>
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diff -r 000000000000 -r f47f5ba2c9be biotradis_filter_tags.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_filter_tags.xml Wed Feb 27 10:54:09 2019 -0500
@@ -0,0 +1,36 @@
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+ Filters a BAM file and outputs reads with tag matching -t option.
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+ macros.xml
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diff -r 000000000000 -r f47f5ba2c9be biotradis_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_plot.xml Wed Feb 27 10:54:09 2019 -0500
@@ -0,0 +1,34 @@
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+ Create insertion site plot for Artemis
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+ macros.xml
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diff -r 000000000000 -r f47f5ba2c9be biotradis_remove_tags.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_remove_tags.xml Wed Feb 27 10:54:09 2019 -0500
@@ -0,0 +1,36 @@
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+ Removes transposon sequence and quality tags from the read strings
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+ macros.xml
+
+
+ $log
+
+ ]]>
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diff -r 000000000000 -r f47f5ba2c9be macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Feb 27 10:54:09 2019 -0500
@@ -0,0 +1,14 @@
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+ 1.4.1
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+ biotradis
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+ 10.1093/bioinformatics/btw022
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+
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