# HG changeset patch
# User iuc
# Date 1547985075 18000
# Node ID 57bf9a0d49a51562881694297693fd2307f5f59f
# Parent 3fd7458bc861065c0943a3aab76326617496c24f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
diff -r 3fd7458bc861 -r 57bf9a0d49a5 alleyoop.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/alleyoop.xml Sun Jan 20 06:51:15 2019 -0500
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+ - post-processing and QC of Slamdunk analyses
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+ macros.xml
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+ alleyoop --version
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+ bams
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+ bams
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+ `_
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+Alleyoop
+========
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+Alleyoop (Additional sLamdunk heLpEr tools for anY diagnOstics Or Plots) is a collection of tools for post-processing and running diagnostics on Slamdunk analyses. This tool works on the output of the **Slamdunk** tool and requires all the inputs listed in the table below.
+
+=============== ==========================================================================================================================================================
+Parameter Description
+=============== ==========================================================================================================================================================
+**Genome** The reference fasta file (Genome assembly).
+**Reference** BED-file containing coordinates for 3' UTRs.
+**Reads** Slamdunk Filtered BAM files.
+**Counts** Slamdunk Count TSV files.
+**Variants** Slandunk VCF files.
+**Read length** Maximum length of reads (usually 50, 100, 150).
+=============== ==========================================================================================================================================================
+
+This tool runs the **Alleyoop** *summary*, *rates*, *utrrates*, *tcperreadpos* and *tcperutrpos* modules and outputs:
+
+* Tab-separated *summary* files from the summary module with mapping and PCA statistics
+* Tab-separated *stats* files from the rates, utrrates, tcperreadpos and tcperutrpos modules
+
+Optionally, the *read-separator* module can be run to output BAM files of separated T>C and non T>C reads.
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+The summary and stats files can be summarised and visualised with MultiQC. An example MultiQC report can be seen here_. For information on these modules see the `Alleyoop documentation`_.
+
+.. _`Alleyoop documentation`: http://t-neumann.github.io/slamdunk/docs.html#document-Alleyoop
+.. _here: http://t-neumann.github.io/slamdunk/multiqc_example/multiqc_report.html
+
+ ]]>
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diff -r 3fd7458bc861 -r 57bf9a0d49a5 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Jan 20 06:51:15 2019 -0500
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+ 0.3.3
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+ slamdunk
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+ @misc{Neumann2018,
+ author = {Neumann, Tobias},
+ year = {2018},
+ title = Slamdunk},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/t-neumann/slamdunk},
+}
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+
+
\ No newline at end of file
diff -r 3fd7458bc861 -r 57bf9a0d49a5 slamdunk.xml
--- a/slamdunk.xml Thu Oct 11 20:33:07 2018 -0400
+++ b/slamdunk.xml Sun Jan 20 06:51:15 2019 -0500
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+
- streamlining SLAM-seq analysis with ultra-high sensitivity
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- slamdunk
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+ macros.xml
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+
slamdunk --version
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help="Maximum read length (before trimming)." />
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+
C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
============================ ================================================================================
+.. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
]]>
-
- @misc{Neumann2018,
- author = {Neumann, Tobias},
- year = {2018},
- title = Slamdunk},
- publisher = {GitHub},
- journal = {GitHub repository},
- url = {https://github.com/t-neumann/slamdunk},
-}
-
+
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1.bam
Binary file test-data/reads1.bam has changed
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_TCReads.bam
Binary file test-data/reads1_TCReads.bam has changed
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_backgroundReads.bam
Binary file test-data/reads1_backgroundReads.bam has changed
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_overallrates.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads1_overallrates.csv Sun Jan 20 06:51:15 2019 -0500
@@ -0,0 +1,7 @@
+# slamdunk rates v0.3.3
+ A a C c G g T t N n
+A 93 20 0 0 0 1 0 0 0 0
+C 0 0 106 12 0 0 0 0 0 0
+G 0 0 0 0 82 33 0 0 0 0
+T 0 0 4 1 0 0 102 47 0 0
+N 0 0 0 0 0 0 0 0 0 0
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_snp.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads1_snp.vcf Sun Jan 20 06:51:15 2019 -0500
@@ -0,0 +1,25 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO== 15">
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT== 15">
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
+chr5 120498 . T C . . . . .
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_tcount.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads1_tcount.tsv Sun Jan 20 06:51:15 2019 -0500
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+Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper
+chr5 120498 121492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0
+chr5 120498 122492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads2.bam
Binary file test-data/reads2.bam has changed
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads2_snp.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads2_snp.vcf Sun Jan 20 06:51:15 2019 -0500
@@ -0,0 +1,25 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO== 15">
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT== 15">
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
+chr5 120499 . T C . . . . .
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads2_tcount.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads2_tcount.tsv Sun Jan 20 06:51:15 2019 -0500
@@ -0,0 +1,3 @@
+Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper
+chr5 120498 121492 Actb 1994 + 0.0227272727273 1000000.0 445 88 2 6 3 0 -1.0 -1.0
+chr5 120498 122492 Actb 1994 + 0.0227272727273 1000000.0 445 88 2 6 3 0 -1.0 -1.0
diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary.txt Sun Jan 20 06:51:15 2019 -0500
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+# slamdunk summary v0.3.3
+FileName SampleName SampleType SampleTime Sequenced Mapped Deduplicated MQ-Filtered Identity-Filtered NM-Filtered Multimap-Filtered Retained Counted Annotation
+./filter/reads1.bam sample_1 NA -1 12 12 0 0 0 0 0 12 16
+./filter/reads2.bam sample_2 NA -1 6 6 0 0 0 0 0 6 12