Mercurial > repos > yhoogstrate > fastq_replace_dots_for_n

changeset 6:a776dd3b437c draft

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Uploaded
author yhoogstrate
date Thu, 13 Nov 2014 11:22:13 -0500
parents c3a676a14734
children 89b13f88bbef
files FASTQ_replace_dots_for_N FASTQ_replace_dots_for_N.py FASTQ_replace_dots_for_N.xml README tool_dependencies.xml
diffstat 5 files changed, 122 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- /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")
--- 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")
--- 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 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="FASTQ_replace_dots_for_N" name="FASTQ_replace_dots_for_N">
+<tool id="FASTQ_replace_dots_for_N" name="FASTQ_replace_dots_for_N" version="1.0.0.a">
 	<description>Replace DOTs for Ns in sequences in FASTQ files.</description>
+	
+	<requirements>
+		<requirement type="package" version="1.0.0">FASTQ_replace_dots_for_N</requirement>
+	</requirements>
+	
 	<command interpreter="python">
 		FASTQ_replace_dots_for_N.py $input > $output
 	</command>
@@ -14,6 +19,22 @@
 	</outputs>
 	
 	<help>
-		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/
 	</help>
-</tool>
+</tool>
\ No newline at end of file
--- /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: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools>
+
+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 repository:
+
+<http://toolshed.dtls.nl/>
+
+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 <http://www.gnu.org/licenses/>.
+
+**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 <http://www.gnu.org/licenses/>.
--- /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 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<!-- @todo: Add dependency of BioPython :: SeqIO -->
+	<package name="FASTQ_replace_dots_for_N" version="1.0.0">
+		<install version="1.0">
+			<actions>
+				<action type="move_file">
+					<source>$REPOSITORY_INSTALL_DIR/FASTQ_replace_dots_for_N</source>
+					<destination>$INSTALL_DIR/bin/</destination>
+				</action>
+				<action type="chmod">
+					<file mode="755">$INSTALL_DIR/bin/FASTQ_replace_dots_for_N</file>
+				</action>
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+	</package>
+</tool_dependency>