# HG changeset patch
# User mcharles
# Date 1410359041 14400
# Node ID 7f36bd1293214e27dfccada5d6e4aef1e547bb9b
# Parent  442a7c88b88631bf9726a3cbfe1c5e83c1e499d2
Uploaded

diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-1x.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-1x.ga	Wed Sep 10 09:18:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,590 +0,0 @@
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\ No newline at end of file
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_2x.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_2x.ga	Wed Sep 10 09:18:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1014 +0,0 @@
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diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_4x.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_4x.ga	Wed Sep 10 09:18:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1564 +0,0 @@
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diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-1x.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-1x.ga	Wed Sep 10 10:24:01 2014 -0400
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diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_2x.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_2x.ga	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,1014 @@
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diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_4x.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_4x.ga	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,1564 @@
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+            "tool_id": "ParseBlastForUniqueMatch", 
+            "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "38": {
+            "annotation": "", 
+            "id": 38, 
+            "input_connections": {
+                "input_blast_file": {
+                    "id": 34, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 28, 
+                    "output_name": "output_file2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ParseBlastForUniqueMatch", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4284.5, 
+                "top": 904
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "ParseBlastForUniqueMatch", 
+            "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "39": {
+            "annotation": "", 
+            "id": 39, 
+            "input_connections": {
+                "input_blast_file": {
+                    "id": 35, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 28, 
+                    "output_name": "output_file3"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ParseBlastForUniqueMatch", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4287.5, 
+                "top": 1103
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "ParseBlastForUniqueMatch", 
+            "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "40": {
+            "annotation": "", 
+            "id": 40, 
+            "input_connections": {
+                "input_blast_file": {
+                    "id": 36, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 28, 
+                    "output_name": "output_file4"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ParseBlastForUniqueMatch", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4281.5, 
+                "top": 1305
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "ParseBlastForUniqueMatch", 
+            "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "41": {
+            "annotation": "", 
+            "id": 41, 
+            "input_connections": {
+                "input_file1": {
+                    "id": 37, 
+                    "output_name": "output_file"
+                }, 
+                "input_file2": {
+                    "id": 38, 
+                    "output_name": "output_file"
+                }, 
+                "input_file3": {
+                    "id": 39, 
+                    "output_name": "output_file"
+                }, 
+                "input_file4": {
+                    "id": 40, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MergeFile4x", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 4700, 
+                "top": 841.8833312988281
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "MergeFile4x", 
+            "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file4\": \"null\", \"input_file1\": \"null\", \"input_file2\": \"null\", \"input_file3\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "42": {
+            "annotation": "", 
+            "id": 42, 
+            "input_connections": {
+                "input_file": {
+                    "id": 41, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilterandstat", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "log_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 5056, 
+                "top": 886.8833312988281
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilterandstat", 
+            "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"2\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"10\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"2\\\", \\\"stat_max_depth_min\\\": \\\"100\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.8\\\"\", \"do_stat\": \"\\\"YES\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.08", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "43": {
+            "annotation": "", 
+            "id": 43, 
+            "input_connections": {
+                "input_blast_filtered_part1_file": {
+                    "id": 37, 
+                    "output_name": "output_file"
+                }, 
+                "input_blast_filtered_part2_file": {
+                    "id": 38, 
+                    "output_name": "output_file"
+                }, 
+                "input_blast_filtered_part3_file": {
+                    "id": 39, 
+                    "output_name": "output_file"
+                }, 
+                "input_blast_filtered_part4_file": {
+                    "id": 40, 
+                    "output_name": "output_file"
+                }, 
+                "input_list_filtered_file": {
+                    "id": 27, 
+                    "output_name": "output_file"
+                }, 
+                "input_mpileup_variant_file": {
+                    "id": 26, 
+                    "output_name": "output_file"
+                }, 
+                "input_read1_part1_trimmed_file": {
+                    "id": 7, 
+                    "output_name": "output_read1_file"
+                }, 
+                "input_read1_part2_trimmed_file": {
+                    "id": 8, 
+                    "output_name": "output_read1_file"
+                }, 
+                "input_read1_part3_trimmed_file": {
+                    "id": 9, 
+                    "output_name": "output_read1_file"
+                }, 
+                "input_read1_part4_trimmed_file": {
+                    "id": 10, 
+                    "output_name": "output_read1_file"
+                }, 
+                "input_read1_row_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "input_read2_part1_trimmed_file": {
+                    "id": 7, 
+                    "output_name": "output_read2_file"
+                }, 
+                "input_read2_part2_trimmed_file": {
+                    "id": 8, 
+                    "output_name": "output_read2_file"
+                }, 
+                "input_read2_part3_trimmed_file": {
+                    "id": 9, 
+                    "output_name": "output_read2_file"
+                }, 
+                "input_read2_part4_trimmed_file": {
+                    "id": 10, 
+                    "output_name": "output_read2_file"
+                }, 
+                "input_read2_row_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input_sam_filtered_part1_file": {
+                    "id": 16, 
+                    "output_name": "output_file"
+                }, 
+                "input_sam_filtered_part2_file": {
+                    "id": 17, 
+                    "output_name": "output_file"
+                }, 
+                "input_sam_filtered_part3_file": {
+                    "id": 18, 
+                    "output_name": "output_file"
+                }, 
+                "input_sam_filtered_part4_file": {
+                    "id": 19, 
+                    "output_name": "output_file"
+                }, 
+                "input_sam_row_part1_file": {
+                    "id": 12, 
+                    "output_name": "output"
+                }, 
+                "input_sam_row_part2_file": {
+                    "id": 13, 
+                    "output_name": "output"
+                }, 
+                "input_sam_row_part3_file": {
+                    "id": 14, 
+                    "output_name": "output"
+                }, 
+                "input_sam_row_part4_file": {
+                    "id": 15, 
+                    "output_name": "output"
+                }, 
+                "input_snp_selected_file": {
+                    "id": 42, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "rapsosnp_stats4x", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 5447.5, 
+                "top": 211
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "rapsosnp_stats4x", 
+            "tool_state": "{\"input_blast_filtered_part2_file\": \"null\", \"input_blast_filtered_part3_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_read1_part4_trimmed_file\": \"null\", \"input_read1_part3_trimmed_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_mpileup_variant_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_blast_filtered_part1_file\": \"null\", \"input_sam_row_part4_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\", \"input_read2_part3_trimmed_file\": \"null\", \"input_read2_part4_trimmed_file\": \"null\", \"input_sam_filtered_part3_file\": \"null\", \"input_sam_filtered_part4_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_blast_filtered_part4_file\": \"null\", \"input_sam_row_part3_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_list_filtered_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/MergeFile2x.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeFile2x.pl	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,21 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $in1 = $ARGV[0];
+my $in2 = $ARGV[1];
+
+open(IN1, $in1) or die ("Can't open $in1\n");
+while (my $line = <IN1>){
+	print $line;
+}
+close (IN1);
+
+open(IN2, $in2) or die ("Can't open $in2\n");
+while (my $line = <IN2>){
+	print $line;
+}
+close (IN2);
+
+
+
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/MergeFile2x.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeFile2x.xml	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,34 @@
+<tool id="MergeFile2x" name="MergeFile2x" version="0.01">
+<description>Merge splitted file</description>
+<command interpreter="perl">
+    MergeFile2x.pl $input_file1 $input_file2 > $output_file 
+</command>
+<inputs>
+<param name="out_format" type="select" label="Format">
+	<option value="pileup">pileup</option>
+	<option value="fastq">fastq</option>
+	<option value="fastqsanger">fastqsanger</option>
+	<option value="sam">sam</option>
+	<option value="fasta">fasta</option>
+</param>
+<param name="input_file1"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 1st file from your history"/>
+<param name="input_file2"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 2nd file from your history"/>
+</inputs>
+<outputs>
+<data name="output_file" format="txt" label="MERGE">
+	<change_format>
+		<when input="out_format" value="pileup" format="pileup" />
+		<when input="out_format" value="fastq" format="fastq" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+		<when input="out_format" value="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+	</change_format>
+</data>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/MergeFile4x.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeFile4x.pl	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,34 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $in1 = $ARGV[0];
+my $in2 = $ARGV[1];
+my $in3 = $ARGV[2];
+my $in4 = $ARGV[3];
+
+open(IN1, $in1) or die ("Can't open $in1\n");
+while (my $line = <IN1>){
+	print $line;
+}
+close (IN1);
+
+open(IN2, $in2) or die ("Can't open $in2\n");
+while (my $line = <IN2>){
+	print $line;
+}
+close (IN2);
+
+open(IN3, $in3) or die ("Can't open $in3\n");
+while (my $line = <IN3>){
+	print $line;
+}
+close (IN3);
+
+open(IN4, $in4) or die ("Can't open $in4\n");
+while (my $line = <IN4>){
+	print $line;
+}
+close (IN4);
+
+
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/MergeFile4x.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeFile4x.xml	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,36 @@
+<tool id="MergeFile4x" name="MergeFile4x" version="0.01">
+<description>Merge splitted file</description>
+<command interpreter="perl">
+    MergeFile4x.pl $input_file1 $input_file2 $input_file3 $input_file4 > $output_file 
+</command>
+<inputs>
+<param name="out_format" type="select" label="Format">
+	<option value="pileup">pileup</option>
+	<option value="fastq">fastq</option>
+	<option value="fastqsanger">fastqsanger</option>
+	<option value="sam">sam</option>
+	<option value="fasta">fasta</option>
+</param>
+<param name="input_file1"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 1st file from your history"/>
+<param name="input_file2"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 2nd file from your history"/>
+<param name="input_file3"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 3rd file from your history"/>
+<param name="input_file4"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 4th file from your history"/>
+</inputs>
+<outputs>
+<data name="output_file" format="txt" label="MERGE on ${on_string}">
+	<change_format>
+		<when input="out_format" value="pileup" format="pileup" />
+		<when input="out_format" value="fastq" format="fastq" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+		<when input="out_format" value="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+	</change_format>
+</data>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/rapsosnp_stats.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/rapsosnp_stats.pl	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,215 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $read1_row = $ARGV[0];
+my $read2_row = $ARGV[1];
+
+my $read1_trimmed = $ARGV[2];
+my $read2_trimmed = $ARGV[3];
+
+my $sam_row = $ARGV[4];
+my $sam_filtered = $ARGV[5];
+
+my $mpileup_variant = $ARGV[6];
+
+my $list_filtered = $ARGV[7];
+
+my $blast_filtered = $ARGV[8];
+
+my $snp_selected = $ARGV[9];
+
+
+open(INR1R, $read1_row) or die ("Can't open $read1_row\n");
+my $nbread=0;
+my $nbbase =0;
+while (my $line1=<INR1R>){
+	my $line2 = <INR1R>;
+	my $line3 = <INR1R>;
+	my $line4 = <INR1R>;
+	if ($line1 =~ /^@/){
+		$nbread++;
+		if ($line2=~/([ATGCNX]+)/i){
+			$nbbase += length($1);
+		}
+	}
+}
+print "Row Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n";
+close (INR1R);
+
+open(INR2R, $read2_row) or die ("Can't open $read2_row\n");
+$nbread=0;
+$nbbase =0;
+while (my $line1=<INR2R>){
+	my $line2 = <INR2R>;
+	my $line3 = <INR2R>;
+	my $line4 = <INR2R>;
+	if ($line1 =~ /^@/){
+		$nbread++;
+		if ($line2=~/([ATGCNX]+)/i){
+			$nbbase += length($1);
+		}
+	}
+}
+print "Row Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n";
+close (INR2R);
+
+open(INR1T, $read1_trimmed) or die ("Can't open $read1_trimmed\n");
+$nbread=0;
+$nbbase =0;
+while (my $line1=<INR1T>){
+	my $line2 = <INR1T>;
+	my $line3 = <INR1T>;
+	my $line4 = <INR1T>;
+	if ($line1 =~ /^@/){
+		$nbread++;
+		if ($line2=~/([ATGCNX]+)/i){
+			$nbbase += length($1);
+		}
+		else {
+			print STDERR "$line1\n$line2\n";
+		}
+	}
+}
+print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n";
+close (INR1T);
+
+open(INR2T, $read2_trimmed) or die ("Can't open $read2_trimmed\n");
+$nbread=0;
+$nbbase =0;
+while (my $line1=<INR2T>){
+	my $line2 = <INR2T>;
+	my $line3 = <INR2T>;
+	my $line4 = <INR2T>;
+	if ($line1 =~ /^@/){
+		$nbread++;
+		if ($line2=~/([ATGCNX]+)/i){
+			$nbbase += length($1);
+		}
+		else {
+			print STDERR "$line1\n$line2\n";
+		}
+	}
+}
+print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n";
+close (INR2T);
+
+print "\nSAM row\n";
+open(SAM, $sam_row) or die ("Can't open $sam_row\n");
+my %bitscore;
+while (my $line=<SAM>){
+	if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){
+		my @fields = split(/\s+/,$line);
+		my $bit = $fields[1];
+		if ($bitscore{$bit}){
+			$bitscore{$bit}++;
+		}
+		else {
+			$bitscore{$bit}=1;
+		}
+	}
+}
+
+print "bitscore\t";
+foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) {
+	print $key,"\t*\t";
+}
+print "\n";
+
+print " number \t";
+foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) {
+	print $bitscore{$key},"\t*\t";
+}
+print "\n";
+close (SAM);
+
+print "\nSAM filtered\n";
+open(SAMF, $sam_filtered) or die ("Can't open $sam_filtered\n");
+undef %bitscore;
+while (my $line=<SAMF>){
+	if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){
+		my @fields = split(/\s+/,$line);
+		my $bit = $fields[1];
+		if ($bitscore{$bit}){
+			$bitscore{$bit}++;
+		}
+		else {
+			$bitscore{$bit}=1;
+		}
+	}
+}
+
+print "bitscore\t";
+foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) {
+	print $key,"\t*\t";
+}
+print "\n";
+
+print " number \t";
+foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) {
+	print $bitscore{$key},"\t*\t";
+}
+print "\n";
+close (SAMF);
+
+print "\nMPILEUP variant\n";
+open(MPV, $mpileup_variant) or die ("Can't open $mpileup_variant\n");
+
+my $nbvariant=0;
+while (my $line=<MPV>){
+	my @fields = split(/\s+/,$line);
+	if ($#fields >= 4){
+		my $match = $fields[4];
+		$match =~ s/\$//g; #the read start at this position
+		$match =~ s/\^.//g; #the read end at this position followed by quality char
+		if ($match =~/[ACGTNacgtn]+/){
+			$nbvariant++;
+		}
+	}
+	else {
+		#print STDERR "Erreur : $line\n";
+	}
+}
+
+print "Variant detected :\t$nbvariant\n";
+close (MPV);
+
+
+print "\nMPILEUP filtered without dubious position\n";
+open(LF, $list_filtered) or die ("Can't open $list_filtered\n");
+$nbvariant=0;
+while (my $line=<LF>){
+	$nbvariant++;
+}
+
+print "Variant selected :\t$nbvariant\n";
+close (LF);
+
+print "\nMPILEUP filtered without dubious position and BLAST\n";
+open(BF, $blast_filtered) or die ("Can't open $blast_filtered\n");
+$nbvariant=0;
+while (my $line=<BF>){
+	$nbvariant++;
+}
+
+print "Variant selected :\t$nbvariant\n";
+close (BF);
+
+
+print "\nSNP selected after mpileup filtering : \t";
+open(SNP, $snp_selected) or die ("Can't open $snp_selected\n");
+$nbvariant=0;
+while (my $line=<SNP>){
+	$nbvariant++;
+}
+
+print "$nbvariant\n";
+close (SNP);
+
+
+
+
+
+
+
+
diff -r 442a7c88b886 -r 7f36bd129321 rapsodyn/rapsosnp_stats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/rapsosnp_stats.xml	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,26 @@
+<tool id="rapsosnp_stats" name="rapsosnp_stats" version="0.01">
+<description>Merge best results from Blast</description>
+<command interpreter="perl">
+    rapsosnp_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_file $input_snp_selected_file  > $output_file 
+</command>
+<inputs>
+<param name="input_read1_row_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/>
+<param name="input_read2_row_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/>
+<param name="input_read1_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED file from your history"/>
+<param name="input_read2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED file from your history"/>
+<param name="input_sam_row_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
+<param name="input_sam_filtered_file"  type="data" format="sam" label="Select a suitable input SAM FILTERED file from your history"/>
+<param name="input_mpileup_variant_file"  type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/>
+<param name="input_list_filtered_file"  type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/>
+<param name="input_blast_filtered_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED file from your history"/>
+<param name="input_snp_selected_file"  type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="txt" label="STATS"/>
+</outputs>
+
+
+<help>
+
+</help>
+</tool>