# HG changeset patch
# User yhoogstrate
# Date 1415895733 18000
# Node ID a776dd3b437c34e0fc2d6a137e8df912940b6eb0
# Parent c3a676a147341e348a0b931d1c6f72aff2ea5b29
Uploaded
diff -r c3a676a14734 -r a776dd3b437c FASTQ_replace_dots_for_N
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FASTQ_replace_dots_for_N Thu Nov 13 11:22:13 2014 -0500
@@ -0,0 +1,18 @@
+#!/usr/bin/env python
+
+__version_info__ = ('1', '0', '0', 'alpha')
+__version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3])+"-"+__version_info__[3]
+__author__ = 'Youri Hoogstrate'
+__homepage__ = 'https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools'
+__license__ = 'GNU General Public License v3 (GPLv3)'
+
+import sys
+from Bio import Seq, SeqRecord, SeqIO
+
+if(len(sys.argv) < 2):
+ input_stream = sys.stdin
+else:
+ input_stream = open(sys.argv[1],"r")
+
+for record in SeqIO.parse(input_stream,"fastq-sanger"):
+ SeqIO.write(SeqRecord.SeqRecord(seq=Seq.Seq(str(record.seq).replace(".","N")),letter_annotations=record.letter_annotations,id=record.id,name=record.name,description=record.description),sys.stdout,"fastq-sanger")
diff -r c3a676a14734 -r a776dd3b437c FASTQ_replace_dots_for_N.py
--- a/FASTQ_replace_dots_for_N.py Thu Dec 19 11:10:29 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-from Bio import Seq, SeqRecord, SeqIO
-
-if(len(sys.argv) < 2):
- input_stream = sys.stdin
-else:
- input_stream = open(sys.argv[1],"r")
-
-for record in SeqIO.parse(input_stream,"fastq-sanger"):
- SeqIO.write(SeqRecord.SeqRecord(seq=Seq.Seq(str(record.seq).replace(".","N")),letter_annotations=record.letter_annotations,id=record.id,name=record.name,description=record.description),sys.stdout,"fastq-sanger")
diff -r c3a676a14734 -r a776dd3b437c FASTQ_replace_dots_for_N.xml
--- a/FASTQ_replace_dots_for_N.xml Thu Dec 19 11:10:29 2013 -0500
+++ b/FASTQ_replace_dots_for_N.xml Thu Nov 13 11:22:13 2014 -0500
@@ -1,6 +1,11 @@
-
+Replace DOTs for Ns in sequences in FASTQ files.
+
+
+ FASTQ_replace_dots_for_N
+
+
FASTQ_replace_dots_for_N.py $input > $output
@@ -14,6 +19,22 @@
- FASTQ_replace_dots_for_N
+Contact
+-------
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+
+http://toolshed.dtls.nl/
+
+http://toolshed.g2.bx.psu.edu/
+
+http://testtoolshed.g2.bx.psu.edu/
-
+
\ No newline at end of file
diff -r c3a676a14734 -r a776dd3b437c README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Thu Nov 13 11:22:13 2014 -0500
@@ -0,0 +1,60 @@
+FASTQ_replace_dots_for_N wrapper for Galaxy
+===========================================
+
+Some FASTQ files contain dots (ASCII char 46) instead of N to indicate
+an unknown called base. Replacing these dots back to N often prevents
+programs from crashing.
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+* Repository-Development:
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+
+
+
+License
+-------
+
+**FASTQ_replace_dots_for_N**:
+
+ Copyright (C) 2013-2014 Youri Hoogstrate
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+**This wrapper**:
+
+ Copyright (C) 2013-2014 Youri Hoogstrate
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
diff -r c3a676a14734 -r a776dd3b437c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Nov 13 11:22:13 2014 -0500
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+ $REPOSITORY_INSTALL_DIR/FASTQ_replace_dots_for_N
+ $INSTALL_DIR/bin/
+
+
+ $INSTALL_DIR/bin/FASTQ_replace_dots_for_N
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+