changeset 5:d51c5af7a8fe draft

planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.py	Fri Mar 11 02:02:09 2016 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError, Popen
+import shlex
+import os
+import logging
+log = logging.getLogger( __name__ )
+
+def novo_align(output_filename, index_filename, fwd_file, rev_file ):
+    #novoalign -c 8 -k -d /cip0/research/ajayi/RNA-seq_Analysis_Project_Case_Study/reference/Homo_Sapiens/out/TB_H37Rv.nix
+    #         -f X165_820L8_.R1_val_1.fq  X165_820L8_.R2_val_2.fq -i PE 250,100
+    #         -o SAM '@RG\tID:readgroup\tPU:platform unit\tLB:library' | samtools view -bS - > `pwd`/out/X165_820L8.bam
+    #output_filename = path.join(output_directory, fwd_file.split(".")[0] + ".bam")
+    param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
+    cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format(
+        index_filename,
+        fwd_file,
+        rev_file,
+        param,
+        output_filename)
+    #cmdline = newSplit(cmdline_str)
+
+    os.system(cmdline_str)
+    #try:
+    #check_call(cmdline)
+    #except CalledProcessError:
+    #    print("Error running the nova-align", file=sys.stderr)
+
+def newSplit(value):
+    lex = shlex.shlex(value)
+    lex.quotes = '"'
+    lex.whitespace_split = True
+    lex.commenters = ''
+    return list(lex)
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
+    parser.add_argument('output_filename')
+    parser.add_argument('--index_filename')
+    parser.add_argument('--forward_filename')
+    parser.add_argument('--reverse_filename')
+    args = parser.parse_args()
+   
+    #a dirty way of referencing the file
+    index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1]
+    
+    novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename)
+
+if __name__ == "__main__": main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.xml	Fri Mar 11 02:02:09 2016 -0500
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<tool id="novo_align" name="NOVO ALIGN" version="0.0.1">
+    <description>Tool to run the Novo Align mapping tool</description>
+    <requirements>
+        <requirement type="package" version="1.2">samtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="python">
+        novo_align.py '${out_file}' --index_file ${index1.fields.path} --forward_file ${fastq_input1} --reverse_file ${fastq_input2}
+    </command>
+    <inputs>
+        <param name="fastq_input1" type="data" format="fasta, fastq, fastsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
+        <param name="fastq_input2" type="data" format="fasta, fastq, fastsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+        <param name="index1" type="select" label="Novo-Align Index(FASTA format)">
+            <options from_data_table="novocraft_index"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="bam" name="out_file" />
+    </outputs>
+    <help>Help!</help>
+    <citations>
+        <citation></citation>
+    </citations>
+    <tests>
+        <test>
+        </test>
+    </tests>
+</tool>

--- a/novo_sort.py	Thu Mar 10 15:53:44 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-import argparse
-from subprocess import check_call, CalledProcessError
-from json import load, dump, dumps
-from os import environ, mkdir, makedirs, path
-from os.path import isdir, exists
-import shlex
-import sys
-import logging
-log = logging.getLogger( __name__ )
-
-def novo_sort( bam_filename ):
-    #novosort -c 8 -m 8G -s-f $i > $i".sorted"; done
-    cmdline_str = "novosort -c 8 -m 8G -s -f {}".format( bam_filename )
-    cmdline = newSplit(cmdline_str)
-    try:
-        check_call(cmdline)
-    except CalledProcessError:
-        print("Error running the nova-align", file=sys.stderr)
-
-def newSplit(value):
-    lex = shlex.shlex(value)
-    lex.quotes = '"'
-    lex.whitespace_split = True
-    lex.commenters = ''
-    return list(lex)
-
-def main():
-    parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
-    parser.add_argument('output_filename')
-    parser.add_argument('--bam_filename')
-    args = parser.parse_args()
-   
-    novo_sort(args.bam_filename)
-
-if __name__ == "__main__": main()

--- a/novo_sort.xml	Thu Mar 10 15:53:44 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="utf-8" ?>
-<tool id="novo_sort" name="NOVO SORT" version="0.0.1">
-    <description>Tool to run the Novo Sort mapping tool</description>
-    <requirements>
-        <requirement type="package" version="1.2">samtools</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-    </stdio>
-    <command interpreter="python">
-        novo_sort.py '${out_file}' --bam_filename ${input1}
-    </command>
-    <inputs>
-        <param name="input1" type="data" format="bam" label="Select first set of reads" help="Specify dataset with forward reads"/>
-    </inputs>
-    <outputs>
-        <data format="bam" name="out_file" />
-    </outputs>
-    <help>Help!</help>
-    <citations>
-        <citation></citation>
-    </citations>
-    <tests>
-        <test>
-        </test>
-    </tests>
-</tool>