# HG changeset patch
# User iuc
# Date 1496683631 14400
# Node ID bc7d99f46a5de4d3ea0e767b1246c081fa58eaa2
# Parent f73729b62b51032b31149a26c637ae2aa42f50d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
diff -r f73729b62b51 -r bc7d99f46a5d macros.xml
--- a/macros.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/macros.xml Mon Jun 05 13:27:11 2017 -0400
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- 1.0-r75-dirty
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+ `_, developed by Heng Li at the Broad Institute
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_comp.xml
--- a/seqtk_comp.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_comp.xml Mon Jun 05 13:27:11 2017 -0400
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- get the nucleotide composition of FASTA/Q
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- macros.xml
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- get the nucleotide composition of FASTA/Q
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+ macros.xml
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+ $default]]>
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_cutN.xml
--- a/seqtk_cutN.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_cutN.xml Mon Jun 05 13:27:11 2017 -0400
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- cut sequence at long N
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- macros.xml
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- cut sequence at long N
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+ macros.xml
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+ $default]]>
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+ test:29-33
ACATG
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@ATTRIBUTION@
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_dropse.xml
--- a/seqtk_dropse.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_dropse.xml Mon Jun 05 13:27:11 2017 -0400
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- drop unpaired from interleaved Paired End FASTA/Q
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- macros.xml
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- drop unpaired from interleaved Paired End FASTA/Q
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+ macros.xml
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+ '$default'
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_fqchk.xml
--- a/seqtk_fqchk.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_fqchk.xml Mon Jun 05 13:27:11 2017 -0400
@@ -1,29 +1,31 @@
- fastq QC (base/quality summary)
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- macros.xml
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- fastq QC (base/quality summary)
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+ macros.xml
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+ $default]]>
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_hety.xml
--- a/seqtk_hety.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_hety.xml Mon Jun 05 13:27:11 2017 -0400
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- regional heterozygosity
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- macros.xml
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- regional heterozygosity
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+ macros.xml
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+ $default]]>
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+ `__ and it will be corrected
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_listhet.xml
--- a/seqtk_listhet.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_listhet.xml Mon Jun 05 13:27:11 2017 -0400
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- extract the position of each het
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- extract the position of each het
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_mergefa.xml
--- a/seqtk_mergefa.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_mergefa.xml Mon Jun 05 13:27:11 2017 -0400
@@ -1,47 +1,48 @@
- merge two FASTA/Q files
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- macros.xml
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- merge two FASTA/Q files
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+ macros.xml
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+ $default]]>
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_mergepe.xml
--- a/seqtk_mergepe.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_mergepe.xml Mon Jun 05 13:27:11 2017 -0400
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- interleave two unpaired FASTA/Q files for a paired-end file
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- macros.xml
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_mutfa.xml
--- a/seqtk_mutfa.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_mutfa.xml Mon Jun 05 13:27:11 2017 -0400
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- point mutate FASTA at specified positions
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- point mutate FASTA at specified positions
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_randbase.xml
--- a/seqtk_randbase.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_randbase.xml Mon Jun 05 13:27:11 2017 -0400
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- choose a random base from hets
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- choose a random base from hets
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_sample.xml
--- a/seqtk_sample.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_sample.xml Mon Jun 05 13:27:11 2017 -0400
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random subsample of fasta or fastq sequences
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+ `__.
+Takes a random subsample of FASTA or FASTQ sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 `__.
The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
@ATTRIBUTION@
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_seq.xml
--- a/seqtk_seq.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_seq.xml Mon Jun 05 13:27:11 2017 -0400
@@ -1,22 +1,23 @@
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- common transformation of FASTA/Q
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- macros.xml
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+ common transformation of FASTA/Q
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_subseq.xml
--- a/seqtk_subseq.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_subseq.xml Mon Jun 05 13:27:11 2017 -0400
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- extract subsequences from FASTA/Q files
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- extract subsequences from FASTA/Q files
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diff -r f73729b62b51 -r bc7d99f46a5d seqtk_trimfq.xml
--- a/seqtk_trimfq.xml Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_trimfq.xml Mon Jun 05 13:27:11 2017 -0400
@@ -1,63 +1,65 @@
- trim FASTQ using the Phred algorithm
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- macros.xml
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- trim FASTQ using the Phred algorithm
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diff -r f73729b62b51 -r bc7d99f46a5d tool_dependencies.xml
--- a/tool_dependencies.xml Fri Jan 01 14:49:42 2016 -0500
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