# HG changeset patch
# User mcharles
# Date 1412773613 14400
# Node ID 7b8646f46010c567efacff760f04ea26209c8a4d
# Parent  fefe6d89dbf1dd28886a453b972b9666b839ae83
Uploaded

diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-1x.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-1x.ga	Wed Sep 10 08:10:38 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 fefe6d89dbf1 -r 7b8646f46010 rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_2x.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_2x.ga	Wed Sep 10 08:10:38 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1014 +0,0 @@
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diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_4x.ga
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_4x.ga	Wed Sep 10 08:10:38 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1564 +0,0 @@
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diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga	Wed Oct 08 09:06:53 2014 -0400
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diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_1x_-_sam.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_1x_-_sam.ga	Wed Oct 08 09:06:53 2014 -0400
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+                    "type": "fasta"
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+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "PrepareFastqLight", 
+            "outputs": [
+                {
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+                    "type": "fastqsanger"
+                }, 
+                {
+                    "name": "output_read2_file", 
+                    "type": "fastqsanger"
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+            "inputs": [], 
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+            }, 
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+            "name": "Map with BWA for Illumina", 
+            "outputs": [
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+                    "type": "sam"
+                }
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+                    "id": 7, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "filtersam_mapped_and_unique", 
+            "outputs": [
+                {
+                    "name": "output_sam_file", 
+                    "type": "sam"
+                }, 
+                {
+                    "name": "log_file", 
+                    "type": "txt"
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+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1411.066650390625, 
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+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
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+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 9, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
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+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"0\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input_pileup_file": {
+                    "id": 10, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "PileupVariant", 
+            "outputs": [
+                {
+                    "name": "output_pileup_file", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "log_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1964.5999755859375, 
+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "PileupVariant", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_pileup_file\": \"null\"}", 
+            "tool_version": "1.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input_list1": {
+                    "id": 11, 
+                    "output_name": "output_pileup_file"
+                }, 
+                "input_list2": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "listfiltering", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "log_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2292.366668701172, 
+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "listfiltering", 
+            "tool_state": "{\"__page__\": 0, \"input_list2\": \"null\", \"input_list1\": \"null\", \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"type\": \"\\\"specific\\\"\"}", 
+            "tool_version": "1.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "input_assembly_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "input_variant_file": {
+                    "id": 12, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "extractseq", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 2561.133331298828, 
+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "extractseq", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}", 
+            "tool_version": "1.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
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+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "db_opts|histdb": {
+                    "id": 6, 
+                    "output_name": "outfile"
+                }, 
+                "query": {
+                    "id": 13, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ blastn", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 2888.8999938964844, 
+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", 
+            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "input_blast_file": {
+                    "id": 14, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 12, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ParseBlastForUniqueMatch", 
+            "outputs": [
+                {
+                    "name": "output_variant_file", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "log_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 3190.6666870117188, 
+                "top": 221
+            }, 
+            "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": "1.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "input_file": {
+                    "id": 15, 
+                    "output_name": "output_variant_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilterandstat", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "log_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 3518.433349609375, 
+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilterandstat", 
+            "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"4\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"200\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.2\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.0\\\"\", \"min_depth\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"500\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "input_files": [
+                    {
+                        "id": 16, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 15, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 12, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 11, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 8, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 5, 
+                        "output_name": "log_file"
+                    }
+                ]
+            }, 
+            "inputs": [], 
+            "name": "MergeMultiFile", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 3846.199951171875, 
+                "top": 221
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput_file": {
+                    "action_arguments": {
+                        "newname": "LOGS"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "MergeMultiFile", 
+            "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}", 
+            "tool_version": "1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/MergeMultiFile.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeMultiFile.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -0,0 +1,15 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+
+my @files = split(/,/,$ARGV[0]);
+for (my $i=0;$i<=$#files;$i++){
+	
+	open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n");
+	while (my $line = <IN>){
+		print $line;
+	}
+	close (IN);
+}
+
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/MergeMultiFile.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeMultiFile.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -0,0 +1,34 @@
+<tool id="MergeMultiFile" name="MergeMultiFile" version="1.00">
+<description>Merge multiple files</description>
+<command interpreter="perl">
+    MergeMultiFile.pl $input_files > $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>
+	<option value="txt">txt</option>
+</param>
+<param name="input_files"  type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" multiple="true" label="Select suitable files 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 fefe6d89dbf1 -r 7b8646f46010 rapsodyn/MergeSamFiles.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeSamFiles.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -0,0 +1,32 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+
+my $header_done = 0;
+my @files = split(/,/,$ARGV[0]);
+for (my $i=0;$i<=$#files;$i++){
+	open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n");
+	while (my $line = <IN>){
+		if ($line =~ /^\@PG\s/){
+			if ($header_done == 0){
+				$header_done = 1;
+				print $line;
+			}
+			else {
+			}
+		}
+		elsif ($line =~ /^\@SQ\s/){
+			if ($header_done == 0){
+				print $line;
+			}
+			else {
+			}
+		}
+		else{
+			print $line;
+		}
+	}
+	close (IN);
+}
+
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/MergeSamFiles.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeSamFiles.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -0,0 +1,18 @@
+<tool id="MergeSamFiles" name="MergeSamFiles" version="1.00">
+<description>Merge multiple SAM files</description>
+<command interpreter="perl">
+    MergeSamFiles.pl $input_files > $output_file 
+</command>
+<inputs>
+<param name="input_files"  type="data" format="sam" multiple="true" label="Select suitable SAM files from your history"/>
+</inputs>
+<outputs>
+<data name="output_file" format="sam" label="MERGE on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/ParseBlastForUniqueMatch.pl
--- a/rapsodyn/ParseBlastForUniqueMatch.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/ParseBlastForUniqueMatch.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,13 +1,26 @@
 #!/usr/bin/perl
+#V1.0.1 added log, option parameters
 use strict;
 use warnings;
+use Getopt::Long;
 
 
-my $input_variant_file = $ARGV[0];
-my $input_blast_file = $ARGV[1];
-my $window_length = $ARGV[2];
-my $nb_mismatch_max = $ARGV[3];
+my $input_variant_file;
+my $input_blast_file;
+my $log_file;
+my $WINDOW_LENGTH= 50;
+my $NB_MISMATCH_MAX = 3;
 
+GetOptions (
+"input_variant_file=s" => \$input_variant_file,
+"input_blast_file=s" => \$input_blast_file,
+"window_length=s" => \$WINDOW_LENGTH,
+"log_file=s" => \$log_file,
+"nb_mismatch_max=s" => \$NB_MISMATCH_MAX
+) or die("Error in command line arguments\n");
+
+my $nb_variant_checked=0;
+my $nb_variant_selected=0;
 my %hash_name;
 
 open(INB, $input_blast_file) or die ("Can't open $input_blast_file\n");
@@ -71,7 +84,7 @@
 	my $nb_gap_query=0;
 	
 	if (length($query_aln) == length($subject_aln)){
-		if (length($query_aln)<$window_length-$nb_mismatch_max){
+		if (length($query_aln)<$WINDOW_LENGTH-$NB_MISMATCH_MAX){
 		}
 		else {
 			my @q = split(//,$query_aln);
@@ -79,27 +92,27 @@
 			for (my $i=0;$i<=$#q;$i++){
 				my $global_idx = $query_start-1+$i-$nb_gap_query;
 				if ($q[$i] eq "-"){
-					if ($global_idx < $window_length){
+					if ($global_idx < $WINDOW_LENGTH){
 						$compt_mismatch_5p++;
 					}
-					elsif ($global_idx > $window_length){
+					elsif ($global_idx > $WINDOW_LENGTH){
 						$compt_mismatch_3p++;
 					}
 					$nb_gap_query++; #On compte les gap dans la query pour les soustraire de l'index global
 				}
 				else {
 					if ($q[$i] ne $s[$i]){
-						if ($global_idx < $window_length){
+						if ($global_idx < $WINDOW_LENGTH){
 							$compt_mismatch_5p++;
 						}
-						elsif ($global_idx > $window_length){
+						elsif ($global_idx > $WINDOW_LENGTH){
 							$compt_mismatch_3p++;
 						}
 					}
 				}
 			}
 			$compt_mismatch_5p += $query_start-1;
-			$compt_mismatch_3p += $window_length *2 + 1 - $query_stop;
+			$compt_mismatch_3p += $WINDOW_LENGTH *2 + 1 - $query_stop;
 			
 			# for (my $i=0;$i<$window_length;$i++){
 				# if ($tbl_q_aln[$i] eq "#"){
@@ -122,7 +135,7 @@
 				# else {
 				# }
 			# }
-			if (($compt_mismatch_5p <= $nb_mismatch_max)||($compt_mismatch_3p <= $nb_mismatch_max)){
+			if (($compt_mismatch_5p <= $NB_MISMATCH_MAX)||($compt_mismatch_3p <= $NB_MISMATCH_MAX)){
 				$hash_name{$name}++;
 			}
 			
@@ -151,6 +164,7 @@
 open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n");
 
 while (my $ligne = <INV>) {
+	$nb_variant_checked++;
 	
 	my @champs = split (/\s+/,$ligne);
 	my $header = $champs[0]."_".$champs[1];
@@ -158,6 +172,7 @@
 	if ($hash_name{$header}){
 		if ($hash_name{$header}==1){
 			print $ligne;
+			$nb_variant_selected++;
 		}
 	}
 	else {
@@ -169,6 +184,12 @@
 
 close(INV);
 
+open (LF,">$log_file") or die("Can't open $log_file\n");
+print LF "\n####\t Blast filtering \n";
+print LF "Variant checked  :\t$nb_variant_checked\n";
+print LF "Variant selected :\t$nb_variant_selected\n";
+close (LF);
+
 
 # foreach my $key (sort keys %hash_name){
 	# print $key,"\t",$hash_name{$key},"\n";
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/ParseBlastForUniqueMatch.xml
--- a/rapsodyn/ParseBlastForUniqueMatch.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/ParseBlastForUniqueMatch.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,16 +1,17 @@
-<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01">
+<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01">
 <description>Filter mpileup with blast results</description>
 <command interpreter="perl">
-    ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file 
+    ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file 
 </command>
 <inputs>
-<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
-<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
-<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
-<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
+	<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
+	<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
+	<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
+	<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
 </inputs>
 <outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="output_variant_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/PileupVariant.pl
--- a/rapsodyn/PileupVariant.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/PileupVariant.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,19 +1,41 @@
 #!/usr/bin/perl
+#V1.0.1 added log, option parameters
 use strict;
+use warnings;
+use Getopt::Long;
 
-my $inputfile = $ARGV[0];
-open(IF, $inputfile)  or die("Can't open $inputfile\n");
+my $input_pileup_file;
+my $output_pileup_file;
+my $log_file;
+
+my $nb_base_covered=0;
+my $nb_variant=0;
+GetOptions (
+"input_pileup_file=s" => \$input_pileup_file,
+"log_file=s" => \$log_file
+) or die("Error in command line arguments\n");
+
+open(IN, $input_pileup_file) or die ("Can't open $input_pileup_file\n");
 
 #Extraction des variants
 my $nb_line=0;
-while (my $line=<IF>){
-	my $test = $line;
-	$test =~ s/\$//g; #the read start at this position
-	$test =~ s/\^.//g; #the read end at this position followed by quality char
-	my @field = split(/\s+/,$test);
+while (my $line=<IN>){
+	#print $line;
+	$nb_base_covered++;
+	$line =~ s/\$//g; #the read start at this position
+	$line =~ s/\^.//g; #the read end at this position followed by quality char
+	#print $line;
 	
+	my @field = split(/\s+/,$line);
 	if ($field[4]=~/[ATGCN]/i){
 		print $line;
+		$nb_variant++;
 	}
 }
-close(IF);
+close(IN);
+
+open (LF,">$log_file") or die("Can't open $log_file\n");
+print LF "\n####\t Variant extraction \n";
+print LF "Position covered :\t$nb_base_covered\n";
+print LF "Variant detected :\t$nb_variant\n";
+close (LF);
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/PileupVariant.xml
--- a/rapsodyn/PileupVariant.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/PileupVariant.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,13 +1,14 @@
-<tool id="PileupVariant" name="PileupVariant" version="0.01">
+<tool id="PileupVariant" name="PileupVariant" version="1.01">
 <description>Keep only mpileup line with variant</description>
 <command interpreter="perl">
-    PileupVariant.pl $input_file > $output_file 
+    PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file 
 </command>
 <inputs>
-<param name="input_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
+	<param name="input_pileup_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
 </inputs>
 <outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>	
 </outputs>
 
 <help>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/PrepareFastqLight.pl
--- a/rapsodyn/PrepareFastqLight.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/PrepareFastqLight.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,28 +1,51 @@
 #!/usr/bin/perl
+#V1.0.1 added log, option parameters
 use strict;
 use warnings;
-
-my $read1 = $ARGV[0];
-my $read2 = $ARGV[1];
+use Getopt::Long;
 
-my $output1 = $ARGV[2];
-my $output2 = $ARGV[3];
+my $read1_file;
+my $read2_file;
+my $log_file;
+my $output1_file;
+my $output2_file;
 
-my $TYPE = $ARGV[4];
-my $MIN_LENGTH = $ARGV[5];
-my $MIN_QUALITY = $ARGV[6];
+my $TYPE="sanger";
+my $MIN_LENGTH=30;
+my $MIN_QUALITY=30;
+
+my $VERBOSE = "OFF";
 
-my $VERBOSE = $ARGV[7];
+GetOptions (
+"read1_file=s" => \$read1_file,
+"read2_file=s" => \$read2_file,
+"log_file=s" => \$log_file,
+"output1_file=s" => \$output1_file,
+"output2_file=s" => \$output2_file,
+"type=s" => \$TYPE,
+"min_length=i" => \$MIN_LENGTH,
+"min_quality=i" => \$MIN_QUALITY,
+"verbose=s" => \$VERBOSE
+) or die("Error in command line arguments\n");
 
-if (!$VERBOSE){
-	$VERBOSE ="OFF";
-}
 
-open(READ1, $read1) or die ("Can't open $read1\n");
-open(READ2, $read2) or die ("Can't open $read2\n");
-open(OUT1, ">$output1") or die ("Can't open $output1\n");
-open(OUT2, ">$output2") or die ("Can't open $output2\n");
+my $nb_read1=0;
+my $nb_base_read1=0;
+my $nb_read2=0;
+my $nb_base_read2=0;
 
+my $nb_read1_t=0;
+my $nb_base_read1_t=0;
+my $nb_read2_t=0;
+my $nb_base_read2_t=0;
+
+my $nb_base_current_t=0;
+
+
+open(READ1, $read1_file) or die ("Can't open $read1_file\n");
+open(READ2, $read2_file) or die ("Can't open $read2_file\n");
+open(OUT1, ">$output1_file") or die ("Can't open $output1_file\n");
+open(OUT2, ">$output2_file") or die ("Can't open $output2_file\n");
 
 my $error1=0;
 my $error2=0;
@@ -43,6 +66,9 @@
 	my $ligne2_r2 =<READ2>;
 	my $ligne3_r2 =<READ2>;
 	my $ligne4_r2 =<READ2>;
+
+	$nb_read1++;
+	$nb_read2++;
 	
 #@ 1 sec
 	if ((!$ligne1_r1)||(!$ligne2_r1)||(!$ligne3_r1)||(!$ligne4_r1)||(!$ligne1_r2)||(!$ligne2_r2)||(!$ligne3_r2)||(!$ligne4_r2)){
@@ -91,6 +117,7 @@
 		my $header2="";
 		my $repheader1="";
 		my $repheader2="";
+
 		
 		if ($ligne1_r1 =~/^\@(.*?)\#/){
 			$header1 = $1;
@@ -190,9 +217,11 @@
 			### Parsing sequence & qualité
 			if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){
 				$seq1 = $1;
+				$nb_base_read1 += length($seq1);
 			}
 			if ($ligne2_r2 =~ /^([ATGCNX]+)\s*$/i){
 				$seq2 = $1;
+				$nb_base_read2 += length($seq2);
 			}
 			if ($ligne4_r1 =~ /^(.*)\s*$/i){
 				$qual1 = $1;
@@ -236,147 +265,155 @@
 			else {
 				my $fastq_lines_r1="";
 				my $fastq_lines_r2="";
+				my $nb_base_current_read1_t = 0;
+				my $nb_base_current_read2_t = 0;
+				
 				$fastq_lines_r1 = &grooming_and_trimming($ligne1_r1,$seq1,$qual1);
+				$nb_base_current_read1_t = $nb_base_current_t;
 				if ($fastq_lines_r1){
 					$fastq_lines_r2 = &grooming_and_trimming($ligne1_r2,$seq2,$qual2);
+					$nb_base_current_read2_t = $nb_base_current_t;
 				}
 				if ($fastq_lines_r2){
 					print OUT1 $fastq_lines_r1;
 					print OUT2 $fastq_lines_r2;
+
+					$nb_read1_t++;
+					$nb_read2_t++;
+					$nb_base_read1_t += $nb_base_current_read1_t;
+					$nb_base_read2_t += $nb_base_current_read2_t;
+
+
 				}
 			}
 		}
 	
-		# print OUT1 $ligne1_r1;
-		# print OUT1 $ligne2_r1;
-		# print OUT1 $ligne3_r1;
-		# print OUT1 $ligne4_r1;
-		# print OUT2 $ligne1_r2;
-		# print OUT2 $ligne2_r2;
-		# print OUT2 $ligne3_r2;
-		# print OUT2 $ligne4_r2;
-		
+
 #@ 7 sec
 	}
 }
 
-
-
 close (READ1);
 close (READ2);
 close (OUT1);
 close (OUT2);
 
-
-
+open (LF,">$log_file") or die("Can't open $log_file\n");
+print LF "\n####\t Fastq preparation \n";
+print LF "## Before preparation\n";
+print LF "#Read1 :\t$nb_read1\t#Base :\t$nb_base_read1\n";
+print LF "#Read2 :\t$nb_read2\t#Base :\t$nb_base_read2\n";
+print LF "## After preparation\n";
+print LF "#Read1 :\t$nb_read1_t\t#Base :\t$nb_base_read1_t\n";
+print LF "#Read2 :\t$nb_read2_t\t#Base :\t$nb_base_read2_t\n";
+close (LF);
+		
 
 sub grooming_and_trimming{
 	my $header = shift;
 	my $seq = shift;
 	my $quality = shift;
 	my $quality_converted="";
+	my $quality_ori=$quality;
 	
-	my $startnoN = 0;
-	my $stopnoN = length($quality)-1;
+	my $lengthseq = length($seq);
+	my $startTrim = 0;
+	my $stopTrim = length($quality)-1;
+	my $startnoN = $startTrim;
+	my $stopnoN = $stopTrim;
 	
-	#print "SEQ :\n$seq\n";
 	
 	my $chercheN = $seq;
-	my @bad_position;
+	my @bad_position_N;
+	my @bad_position_Q;
 	my $current_index = index($chercheN,"N");
 	my $abs_index = $current_index;
 	while ($current_index >=0){
-		push (@bad_position,$abs_index);
+		push (@bad_position_N,$abs_index);
 
 		if ($current_index<length($seq)){
 			$chercheN = substr($chercheN,$current_index+1);
 			$current_index = index($chercheN,"N");
-			$abs_index = $current_index + $bad_position[$#bad_position]+1;
+			$abs_index = $current_index + $bad_position_N[$#bad_position_N]+1;
 		}
 		else {
 			last;
 		}
 	}
+		
+	my @q = split(//,$quality);
+	for (my $i=0;$i<=$#q;$i++){
+		my $chr = $q[$i];
+		my $num = ord($q[$i]);
+		if ($TYPE eq "illumina"){
+			$num = $num - 31; # 31 comme la difference entre la plage sanger (33-> 93 / 0->60) et illumina (64->104 / 0->40)
+			$quality_converted .= chr($num);
+		}
+		
+		if ($num < $MIN_QUALITY + 33){ #33 comme le départ de la plage sanger
+			push(@bad_position_Q,$i);
+		}
+	}
+	if ($quality_converted){$quality = $quality_converted;}
 	
+	my @bad_position = (@bad_position_N, @bad_position_Q);
 	
 	if ($#bad_position>=0){
-		my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)};
-		$startnoN = $coord{"start"};
-		$stopnoN = $coord{"stop"};	
-	}
-	my $lengthnoN = $stopnoN - $startnoN + 1;
-	my $seqnoN = substr($seq,$startnoN,$lengthnoN);
-	#print "$seqnoN\n";
-	
-	if ($lengthnoN >= $MIN_LENGTH){
-		my $startTrim = $startnoN;
-		my $stopTrim = $stopnoN;
-		
-		my $quality_converted="";
-		my @bad_position;
+		@bad_position = sort {$a <=> $b} @bad_position;
+		my %coord=%{&extract_longer_string_coordinates_from_bad_position(0,$stopTrim,\@bad_position)};
+		$startTrim = $coord{"start"};
+		$stopTrim = $coord{"stop"};
+#print "$startTrim .. $stopTrim\n";
 		
-		my @q = split(//,$quality);
-		#print "QUALITY\n";
-		#print "$quality\n";
-		for (my $i=0;$i<=$stopnoN;$i++){
-			my $chr = $q[$i];
-			my $num = ord($q[$i]);
-			if ($TYPE eq "illumina"){
-				$num = $num -64+33;
-				$quality_converted .= chr($num);
-			}
-			
-			if ($num <$MIN_QUALITY + 64 - 33 ){
-				push(@bad_position,$i+$startnoN);
-			}
-		}
-		if ($quality_converted){$quality = $quality_converted;}
-		#print "$quality\n";
-		
-		
-		
-		if ($#bad_position>=0){
-			# for (my $i=0;$i<=$#bad_position;$i++){
-				# print $bad_position[$i]."\t";
-			# }
-			# print "\n";
-			my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)};
-			$startTrim = $coord{"start"};
-			$stopTrim = $coord{"stop"};
-			#print "$startTrim .. $stopTrim\n";
-			
-		}
-		my $lengthTrim = $stopTrim - $startTrim +1;
-		
-		
-		my $fastq_lines="";
-		
-		if ($lengthTrim >= $MIN_LENGTH){
-			$fastq_lines .= $header;
-			$fastq_lines .= substr($seq,$startTrim,$lengthTrim)."\n";
-			$fastq_lines .= "+\n";
-			$fastq_lines .= substr($quality,$startTrim,$lengthTrim)."\n";
-			return $fastq_lines;
-		}
-		else {
-			return "";
-		}
-		
-		
+	}
+	my $lengthTrim = $stopTrim - $startTrim +1;
+
+	#if ($stats_length{$lengthTrim}){
+	#	$stats_length{$lengthTrim} = 1;		
+	#}
+	#else {
+	#	$stats_length{$lengthTrim}++;
+	#}
+	my $fastq_lines="";
+	
+#	if ($header =~ /GA8\-EAS671_0005\:3\:1\:1043\:4432/){
+#		print "HEAD:\t$header";	
+#		print "SEQ:\n$seq\n";
+#		print "$quality_ori\n";
+#		print "$quality\n";
+#		for (my $i=0;$i<=$#bad_position;$i++){
+#			print $bad_position[$i]."(".$q[$bad_position[$i]]." : ".ord($q[$bad_position[$i]]).")"."\t";
+#		}
+#		print "\n";
+#		print "$startTrim .. $stopTrim / $lengthTrim \n";
+#		print $fastq_lines;
+#		print "\n";
+#	}
+
+	#for (my $i=$startTrim;$i<=$stopTrim;$i++){
+	#	if ($stats_quality{ord($q{$i])}){
+	#		$stats_quality{ord($q{$i])}=1;
+	#	}
+	#	else {
+	#		$stats_quality{ord($q{$i])}++;
+	#	}
+	#}
+
+	if ($lengthTrim >= $MIN_LENGTH){
+		$fastq_lines .= $header;
+		my $new_seq = substr($seq,$startTrim,$lengthTrim);
+		$nb_base_current_t = length($new_seq);
+		$fastq_lines .= $new_seq."\n";
+		$fastq_lines .= "+\n";
+		my $new_q = substr($quality,$startTrim,$lengthTrim);
+		$fastq_lines .= $new_q."\n";
+		return $fastq_lines;
 		
 	}
 	else {
+		#print "Insufficient length after trimming\n";
 		return "";
 	}
-	
-	
-	# my @s = split(//,$seq);
-	# my $sanger_quality="";
-
-	
-	
-
-	# return $sanger_quality;
 }
 
 sub extract_longer_string_coordinates_from_bad_position{
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/PrepareFastqLight.xml
--- a/rapsodyn/PrepareFastqLight.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/PrepareFastqLight.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,21 +1,22 @@
-<tool id="PrepareFastqLight" name="PrepareFastqLight" version="0.01">
+<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.01">
 <description>Fastq preparation</description>
 <command interpreter="perl">
-    PrepareFastqLight.pl $input_read1_file $input_read2_file $output_read1_file $output_read2_file $quality_type $min_quality $min_length
+    PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length
 </command>
 <inputs>
-<param name="input_read1_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/>
-<param name="input_read2_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/>
-<param name="quality_type" type="select" label="Select input quality format">
-   <option value="sanger">Sanger</option>
-   <option value="illumina">Illumina 1.3-1.7</option>
- </param>
-<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/>
-<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/>
+	<param name="input_read1_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/>
+	<param name="input_read2_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/>
+	<param name="quality_type" type="select" label="Select input quality format">
+		<option value="sanger">Sanger</option>
+		<option value="illumina">Illumina 1.3-1.7</option>
+	</param>
+	<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/>
+	<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/>
 </inputs>
 <outputs>
-<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
-<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
+	<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
+	<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/SplitFile10x.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/SplitFile10x.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -0,0 +1,94 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+
+my $in = $ARGV[0];
+my $NB_LINE_GROUP = $ARGV[1];
+my $out1 = $ARGV[2];
+my $out2 = $ARGV[3];
+my $out3 = $ARGV[4];
+my $out4 = $ARGV[5];
+my $out5 = $ARGV[6];
+my $out6 = $ARGV[7];
+my $out7 = $ARGV[8];
+my $out8 = $ARGV[9];
+my $out9 = $ARGV[10];
+my $out10 = $ARGV[11];
+
+my $file_nb = 1;
+
+my @in;
+my $current_aggregate;
+open(IN, $in) or die ("Can't open $in\n");
+while (my $line =<IN>){
+	$current_aggregate = $line;
+	my $nb_line=1;
+	if ($NB_LINE_GROUP>1){
+		while (my $add_line = <IN>){
+			$current_aggregate .= $add_line;
+			$nb_line++;
+			if ($nb_line == $NB_LINE_GROUP){
+				last;
+			}
+		}
+	}	
+	push (@in,$current_aggregate);
+}
+close (IN);
+
+open (OUT1,">$out1") or die ("Can't open $out1");
+open (OUT2,">$out2") or die ("Can't open $out2");
+open (OUT3,">$out3") or die ("Can't open $out3");
+open (OUT4,">$out4") or die ("Can't open $out4");
+open (OUT5,">$out5") or die ("Can't open $out5");
+open (OUT6,">$out6") or die ("Can't open $out6");
+open (OUT7,">$out7") or die ("Can't open $out7");
+open (OUT8,">$out8") or die ("Can't open $out8");
+open (OUT9,">$out9") or die ("Can't open $out9");
+open (OUT10,">$out10") or die ("Can't open $out10");
+
+
+for (my $i=0;$i<=$#in;$i++){
+	if ($i <= $#in * 1 /10){
+		print OUT1 $in[$i];
+	}
+	elsif ($i <= $#in* 2 /10){
+		print OUT2 $in[$i];
+	}
+	elsif ($i <= $#in*3/10){
+		print OUT3 $in[$i];
+	}
+	elsif ($i <= $#in*4/10){
+		print OUT4 $in[$i];
+	}
+	elsif ($i <= $#in*5/10){
+		print OUT5 $in[$i];
+	}
+	elsif ($i <= $#in*6/10){
+		print OUT6 $in[$i];
+	}
+	elsif ($i <= $#in*7/10){
+		print OUT7 $in[$i];
+	}
+	elsif ($i <= $#in*8/10){
+		print OUT8 $in[$i];
+	}
+	elsif ($i <= $#in*9/10){
+		print OUT9 $in[$i];
+	}
+	elsif ($i <= $#in*10/10){
+		print OUT10 $in[$i];
+	}
+	else {
+
+	}
+
+
+}  
+close (OUT1);
+close (OUT2);
+close (OUT3);
+close (OUT4);
+
+
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/SplitFile10x.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/SplitFile10x.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -0,0 +1,116 @@
+<tool id="SplitFile10x" name="SplitFile10x" version="1.00">
+<description>Split file in 10</description>
+<command interpreter="perl">
+    SplitFile10x.pl $input_file $line_number $output_file1 $output_file2 $output_file3 $output_file4 $output_file5 $output_file6 $output_file7 $output_file8 $output_file9 $output_file10
+</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_file"  type="data" format="fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable input file from your history"/>
+<param name="line_number" type="integer" value="4" label="Number of line read at a time before splitting"/>
+</inputs>
+<outputs>
+<data name="output_file1" format="txt" label="PART1 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file2" format="txt" label="PART2 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file3" format="txt" label="PART3 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file4" format="txt" label="PART4 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file5" format="txt" label="PART5 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file6" format="txt" label="PART6 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file7" format="txt" label="PART7 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file8" format="txt" label="PART8 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file9" format="txt" label="PART9 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+<data name="output_file10" format="txt" label="PART10 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="sam" format="sam" />
+		<when input="out_format" value="fasta" format="fasta" />
+		<when input="out_format" value="fastqsanger" format="fastqsanger" />
+	</change_format>
+</data>
+
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/SplitFile2x.pl
--- a/rapsodyn/SplitFile2x.pl	Wed Sep 10 08:10:38 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use warnings;
-
-my $in = $ARGV[0];
-my $NB_LINE_GROUP = $ARGV[1];
-my $NB_FILE = 2;
-my $out1 = $ARGV[2];
-my $out2 = $ARGV[3];
-
-if (!$NB_LINE_GROUP){
-	$NB_LINE_GROUP=4;
-}
-
-if (!$NB_FILE){
-	$NB_FILE=2;
-}
-
-my $file_nb = 1;
-
-my @in;
-my $current_aggregate;
-open(IN, $in) or die ("Can't open $in\n");
-while (my $line =<IN>){
-	$current_aggregate = $line;
-	my $nb_line=1;
-	if ($NB_LINE_GROUP>1){
-		while (my $add_line = <IN>){
-			$current_aggregate .= $add_line;
-			$nb_line++;
-			if ($nb_line == $NB_LINE_GROUP){
-				last;
-			}
-		}
-	}	
-	push (@in,$current_aggregate);
-}
-close (IN);
-
-open (OUT1,">$out1") or die ("Can't open $out1");
-open (OUT2,">$out2") or die ("Can't open $out2");
-
-for (my $i=0;$i<=$#in;$i++){
-	if ($i <= $#in/2){
-		print OUT1 $in[$i];
-	}
-	else {
-		print OUT2 $in[$i];
-	}
-
-
-}  
-close (OUT1);
-close (OUT2);
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/SplitFile2x.xml
--- a/rapsodyn/SplitFile2x.xml	Wed Sep 10 08:10:38 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<tool id="SplitFile2x" name="SplitFile2x" version="0.01">
-<description>Split file in 2</description>
-<command interpreter="perl">
-    SplitFile2x.pl $input_file $line_number $output_file1 $output_file2
-</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_file"  type="data" format="fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable input file from your history"/>
-<param name="line_number" type="integer" value="4" label="Number of line read at a time before splitting"/>
-</inputs>
-<outputs>
-<data name="output_file1" format="txt" label="PART1 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="sam" format="sam" />
-		<when input="out_format" value="fasta" format="fasta" />
-		<when input="out_format" value="fastqsanger" format="fastqsanger" />
-	</change_format>
-</data>
-<data name="output_file2" format="txt" label="PART2 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="sam" format="sam" />
-		<when input="out_format" value="fasta" format="fasta" />
-		<when input="out_format" value="fastqsanger" format="fastqsanger" />
-	</change_format>
-</data>
-
-</outputs>
-
-<help>
-
-
-
-</help>
-</tool>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/extractseq.pl
--- a/rapsodyn/extractseq.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/extractseq.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,5 +1,5 @@
 #!/usr/bin/perl
-#V1.10
+#V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+
 
 use strict;
 use warnings;
@@ -129,4 +129,4 @@
 	else {
 		return $second;
 	}
-}
\ No newline at end of file
+}
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/extractseq.xml
--- a/rapsodyn/extractseq.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/extractseq.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="extractseq" name="extractseq" version="0.03">
+<tool id="extractseq" name="extractseq" version="1.01">
 <description>Extract Sequence around variant position</description>
 <command interpreter="perl">
     extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file 
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/fastaGroomerForMakeBlastdb.pl
--- a/rapsodyn/fastaGroomerForMakeBlastdb.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/fastaGroomerForMakeBlastdb.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,4 +1,5 @@
 #!/usr/bin/perl
+#V1.0.0
 my $inputfasta = $ARGV[0];
 
 open(IB, $inputfasta) or die ("Can't open $inputfasta \n");
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/fastaGroomerForMakeBlastdb.xml
--- a/rapsodyn/fastaGroomerForMakeBlastdb.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/fastaGroomerForMakeBlastdb.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="0.01">
+<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="1.00">
 <description>fasta Groomer For MakeBlastdb</description>
 <command interpreter="perl">
     fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/filtersam_mapped_and_unique.pl
--- a/rapsodyn/filtersam_mapped_and_unique.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/filtersam_mapped_and_unique.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,23 +1,83 @@
 #!/usr/bin/perl
+#V1.0.1 added log, option parameters
 use strict;
 use warnings;
+use Getopt::Long;
 
-open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n");
+my $input_sam_file;
+my $output_sam_file;
+my $log_file;
+
+my %bitscore_all;
+my %bitscore_selected;
+
+GetOptions (
+"input_sam_file=s" => \$input_sam_file,
+"output_sam_file=s" => \$output_sam_file,
+"log_file=s" => \$log_file
+) or die("Error in command line arguments\n");
+
+open(IN, $input_sam_file) or die ("Can't open $input_sam_file\n");
 while (my $line=<IN>){
-	if ($line =~ /^\@/){
+	if (($line =~ /^\@SQ/)||($line =~ /^\@PG/)){
 		#Header conservation
 		print $line;
 	}
 	else {
 		#Optionnal flag verification
+		my @fields_all = split (/\s+/,$line);
+		my $bit = $fields_all[1];
+		if ($bitscore_all{$bit}){
+			$bitscore_all{$bit}++;
+		}
+		else {
+			$bitscore_all{$bit}=1;
+		}
 		if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){
-			my @fields = split (/\s+/,$line);
-			if (($fields[1]==83)||($fields[1]==163)||($fields[1]==147)||($fields[1]==99)){
+			my @fields_selected = split (/\s+/,$line);
+			if (($fields_selected[1]==83)||($fields_selected[1]==163)||($fields_selected[1]==147)||($fields_selected[1]==99)){
 				print $line;
+				my $bit = $fields_selected[1];
+				if ($bitscore_selected{$bit}){
+					$bitscore_selected{$bit}++;
+				}
+				else {
+					$bitscore_selected{$bit}=1;
+				}
 			}
 		}
 	}
 }
 
+close (IN);
 
-close (IN);
\ No newline at end of file
+open (LF,">$log_file") or die("Can't open $log_file\n");
+print LF "\n####\t Sam filtering \n";
+print LF "## Before filtering\n";
+print LF "bitscore\t:\t";
+foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
+	print LF $key,"\t*\t";
+}
+print LF "\n number \t:\t";
+foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
+	print LF $bitscore_all{$key},"\t*\t";
+}
+print LF "\n";
+print LF "## After filtering\n";
+print LF "bitscore\t:\t";
+foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
+	print LF $key,"\t*\t";
+}
+print LF "\n number \t:\t";
+foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
+	print LF $bitscore_selected{$key},"\t*\t";
+}
+print LF "\n";
+close (LF);
+
+
+
+
+
+
+
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/filtersam_mapped_and_unique.xml
--- a/rapsodyn/filtersam_mapped_and_unique.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/filtersam_mapped_and_unique.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,13 +1,14 @@
-<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="0.01">
+<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="1.01">
 <description>Filter SAM file for uniq and well mapped pair-end reads</description>
 <command interpreter="perl">
-    filtersam_mapped_and_unique.pl $input_sam_file > $output_file 
+    filtersam_mapped_and_unique.pl -input_sam_file $input_sam_file -log_file $log_file> $output_sam_file 
 </command>
 <inputs>
-<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
+	<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
 </inputs>
 <outputs>
- <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/>
+	<data name="output_sam_file" format="sam" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/listfiltering.pl
--- a/rapsodyn/listfiltering.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/listfiltering.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,47 +1,51 @@
 #!/usr/bin/perl
+# v1.0.1 added log, and two different type of filtering (common / specific)
 use strict;
 use Getopt::Long;
 
-my $inputfile;
-my $headerfile;
-my $nb_col=1;
+my $list1_file;
+my $list2_file;
+my $log_file;
+my $NB_COL=1;
+my $TYPE = "common";
 my %header;
+my $nb_list1 = 0;
+my $nb_list2 = 0;
+my $nb_common = 0;
 
-if ($#ARGV<0){
-	print "\n";
-	print "perl 021_ListFiltering.pl -input_file <file> -header_file <file> -nb_col <integer>[1]\n";
-	exit(0);
-}
 
 GetOptions (
-"input_file=s" => \$inputfile,
-"header_file=s" => \$headerfile,
-"nb_col=i" => \$nb_col
+"list1_file=s" => \$list1_file,
+"list2_file=s" => \$list2_file,
+"log_file=s" => \$log_file,
+"type=s" => \$TYPE,
+"nb_col=i" => \$NB_COL
 ) or die("Error in command line arguments\n");
 
-open(HF, $headerfile)  or die("Can't open $headerfile\n");
-while (my $line=<HF>){
+open(L2, $list2_file)  or die("Can't open $list2_file\n");
+while (my $line=<L2>){
+	$nb_list2++;
 	chomp($line);
 	my @fields = split(/\s+/,$line);
 	my $ref="";
 	my $compt=0;
-	while ($compt<$nb_col){
+	while ($compt<$NB_COL){
 		if ($ref){$ref.="\t";}
 		$ref.=$fields[$compt];
 		$compt++;
 	}
-	# my $ref = "$fields[0]\t$fields[1]";
 	$header{$ref}=$line;
 }
-close (HF);
+close (L2);
 
 
-open(IF, $inputfile)  or die("Can't open $inputfile\n");
-while (my $line=<IF>){
+open(L1, $list1_file)  or die("Can't open $list1_file\n");
+while (my $line=<L1>){
+	$nb_list1++;
 	my @fields = split(/\s+/,$line);
 	my $ref="";
 	my $compt=0;
-	while ($compt<$nb_col){
+	while ($compt<$NB_COL){
 		if ($ref){$ref.="\t";}
 		$ref.=$fields[$compt];
 		$compt++;
@@ -49,13 +53,34 @@
 	# my $ref = "$fields[0]\t$fields[1]";
 
 	if ($header{$ref}){
-		# print $line;
-		# print $header{$ref},"\n";
+		$nb_common++;
+		if ($TYPE eq "common"){
+			print $line;
+		}
+		elsif ($TYPE eq "specific") {
+		}
+		else {
+		}
 	}
 	else {
-		print $line;
+		if ($TYPE eq "common"){
+		}
+		elsif ($TYPE eq "specific") {
+			print $line;
+		}
+		else {
+		}
 	}
 	
 }
-close(IF);
+my $nb_list1_only = $nb_list1 - $nb_common;
+my $nb_list2_only = $nb_list2 - $nb_common;
 
+close(L1);
+open (LF,">$log_file") or die("Can't open $log_file\n");
+print LF "\n####\t List Filtering \n";
+print LF "#List 1 :\t$nb_list1 ($nb_list1_only)\n";
+print LF "#List 2 :\t$nb_list2 ($nb_list2_only)\n";
+print LF "#Common :\t$nb_common\n";
+close (LF);
+
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/listfiltering.xml
--- a/rapsodyn/listfiltering.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/listfiltering.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,15 +1,20 @@
-<tool id="listfiltering" name="listfiltering" version="0.01">
-<description>Compare listA and listB first X column and remove from listA the elements present in listB</description>
+<tool id="listfiltering" name="listfiltering" version="1.01">
+<description>Compare list1 and list2</description>
 <command interpreter="perl">
-    listfiltering.pl -input_file $input_listA -header_file $input_listB -nb_col $nb_col > $output_file 
+    listfiltering.pl -list1_file $input_list1 -list2_file $input_list2 -nb_col $nb_col -type $type -log_file $log_file > $output_file 
 </command>
 <inputs>
-<param name="input_listA"  type="data" format="pileup" label="Select a suitable input file from your history"/>
-<param name="input_listB"  type="data" format="txt" label="Select a suitable input file from your history"/>
+<param name="input_list1"  type="data" format="txt,pileup" label="Select list1 file from your history"/>
+<param name="input_list2"  type="data" format="txt,pileup" label="Select list2 file from your history"/>
+<param name="type" type="select" label="Select type of filtering">
+	<option value="specific">Only in list1</option>   
+	<option value="common">Common</option>
+</param>
 <param name="nb_col" type="integer" value="2" label="Number of column to compare"/>
 </inputs>
 <outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/mpileupfilterandstat.pl
--- a/rapsodyn/mpileupfilterandstat.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/mpileupfilterandstat.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,4 +1,5 @@
 #!/usr/bin/perl
+#V1.0.0
 use strict;
 use Getopt::Long;
 
@@ -29,6 +30,9 @@
 my $ONLY_UNFILTERED_VARIANT="OFF";
 my $DO_STAT="NO";
 
+my $nb_variant_checked=0;
+my $nb_variant_selected=0;
+
 
 my $STAT_MIN_DEPTH_MIN = 2;
 my $STAT_MIN_DEPTH_MAX = 10;
@@ -83,6 +87,7 @@
 #Extraction des variants
 my $nb_line=0;
 while (my $line=<IF>){
+	$nb_variant_checked++;
 	$nb_line++;
 	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
 		print "$nb_line\n";
@@ -151,6 +156,7 @@
 	my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM);
 	if ($error_code == 0){
 		print $line{"line"};
+		$nb_variant_selected++;
 	}
 	else {
 		push(@error,$error_code,"\t",$line{"line"});
@@ -159,8 +165,12 @@
 
 ### LOG
 open(LF,">$logfile") or die ("Can't open $logfile\n");
-
-if ($DO_STAT eq "YES"){
+print LF "\n####\t MPileup filtering \n";
+print LF "Variant checked  :\t$nb_variant_checked\n";
+if ($DO_STAT eq "NO"){
+	print LF "Variant selected :\t$nb_variant_selected\n";
+}
+elsif ($DO_STAT eq "YES"){
 	for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){
 		for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){
 			for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){ 
@@ -183,9 +193,9 @@
 }
 
 
-for (my $i=0;$i<=$#error;$i++){
-	print LF $error[$i];
-}
+#for (my $i=0;$i<=$#error;$i++){
+#	print LF $error[$i];
+#}
 close (LF);
 
 
diff -r fefe6d89dbf1 -r 7b8646f46010 rapsodyn/mpileupfilterandstat.xml
--- a/rapsodyn/mpileupfilterandstat.xml	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/mpileupfilterandstat.xml	Wed Oct 08 09:06:53 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08">
+<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="1.00">
 <description>Filter mpileup file entry</description>
 <command interpreter="perl">
   #if $stat.do_stat=="YES"
@@ -14,26 +14,26 @@
 </command>
 <inputs>
 <param name="input_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
-<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/>
-<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/>
-<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
+<param name="min_depth" type="integer" value="1" label="Minimum depth at variant position "/>
+<param name="max_depth" type="integer" value="500" label="Maximum depth at variant position "/>
+<param name="min_frequency" type="float" value="0" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
 <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
-<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/>
+<param name="min_distance" type="integer" value="0" label="Minimum physical distance between variant"/>
 <conditional name="stat">
   <param name="do_stat" type="select" label="Compute stats ">
     <option value="NO">NO</option>
     <option value="YES">YES</option>
   </param>
   <when value="YES">
-    <param name="stat_min_depth_min" type="integer" value = "2" label="min_depth - min" />
-    <param name="stat_min_depth_max" type="integer" value = "10" label="min_depth - max" />
-    <param name="stat_min_depth_step" type="integer" value = "2" label="min_depth - step" />
-    <param name="stat_max_depth_min" type="integer" value = "100" label="max_depth - min" />
+    <param name="stat_min_depth_min" type="integer" value = "4" label="min_depth - min" />
+    <param name="stat_min_depth_max" type="integer" value = "20" label="min_depth - max" />
+    <param name="stat_min_depth_step" type="integer" value = "4" label="min_depth - step" />
+    <param name="stat_max_depth_min" type="integer" value = "200" label="max_depth - min" />
     <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" />
     <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" />
     <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" />
     <param name="stat_freq_max" type="float" value = "1" label="freq - max" />
-    <param name="stat_freq_step" type="float" value = "0.1" label="freq - step" />
+    <param name="stat_freq_step" type="float" value = "0.2" label="freq - step" />
     <param name="stat_dist_min" type="integer" value = "0" label="dist - min" />
     <param name="stat_dist_max" type="integer" value = "50" label="dist - max" />
     <param name="stat_dist_step" type="integer" value = "50" label="dist - step" />