# HG changeset patch
# User mcharles
# Date 1408467653 14400
# Node ID 658acc3202dce34c8e862dfbc3f90f09f6c9d0c4
# Parent  b7125d07b446bba395352965ccc7421aacccb6b7
Uploaded

diff -r b7125d07b446 -r 658acc3202dc rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Filtering.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Filtering.ga	Tue Aug 19 13:00:53 2014 -0400
@@ -0,0 +1,424 @@
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\ No newline at end of file
diff -r b7125d07b446 -r 658acc3202dc rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Mapping.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Mapping.ga	Tue Aug 19 13:00:53 2014 -0400
@@ -0,0 +1,114 @@
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\ No newline at end of file
diff -r b7125d07b446 -r 658acc3202dc rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Preparation.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Preparation.ga	Tue Aug 19 13:00:53 2014 -0400
@@ -0,0 +1,260 @@
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diff -r b7125d07b446 -r 658acc3202dc rapsodyn/Galaxy-Workflow-Rapsodyn_v1.4.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Rapsodyn_v1.4.ga	Tue Aug 19 13:00:53 2014 -0400
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+            "input_connections": {
+                "source|input1": {
+                    "id": 13, 
+                    "output_name": "output_file"
+                }, 
+                "source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 2332, 
+                "top": 550.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 14, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 2560, 
+                "top": 550.5
+            }, 
+            "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, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"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\\\": \\\"30\\\", \\\"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\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "input_file": {
+                    "id": 15, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilter", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 2886, 
+                "top": 550.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilter", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"50\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.05", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "input_listA": {
+                    "id": 16, 
+                    "output_name": "output_file"
+                }, 
+                "input_listB": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "listfiltering", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 3214, 
+                "top": 550.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "listfiltering", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"input_listB\": \"null\", \"input_listA\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "18": {
+            "annotation": "", 
+            "id": 18, 
+            "input_connections": {
+                "input_assembly_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "input_variant_file": {
+                    "id": 17, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "extractseq", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 3542, 
+                "top": 550.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "extractseq", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_assembly_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "", 
+            "id": 19, 
+            "input_connections": {
+                "db_opts|histdb": {
+                    "id": 8, 
+                    "output_name": "outfile"
+                }, 
+                "query": {
+                    "id": 18, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "NCBI BLAST+ blastn", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 3870, 
+                "top": 550.5
+            }, 
+            "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\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"blast_type\": \"\\\"megablast\\\"\", \"output\": \"{\\\"out_format\\\": \\\"5\\\", \\\"__current_case__\\\": 3}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.1.00", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "20": {
+            "annotation": "", 
+            "id": 20, 
+            "input_connections": {
+                "input_blastxml_file": {
+                    "id": 19, 
+                    "output_name": "output1"
+                }, 
+                "input_variant_file": {
+                    "id": 17, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilteronblastxml", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 4172, 
+                "top": 550.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilteronblastxml", 
+            "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_blastxml_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.03", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
diff -r b7125d07b446 -r 658acc3202dc rapsodyn/repository_dependencies.xml
--- a/rapsodyn/repository_dependencies.xml	Thu Aug 14 09:39:11 2014 -0400
+++ b/rapsodyn/repository_dependencies.xml	Tue Aug 19 13:00:53 2014 -0400
@@ -7,4 +7,5 @@
      <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
      <repository changeset_revision="9710e9bcc5f3" name="samtools_filter" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" />
      <repository changeset_revision="623f727cdff1" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+     <repository changeset_revision="c70137414dcd" name="sickle" owner="nikhil-joshi" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>
diff -r b7125d07b446 -r 658acc3202dc rapsodyn/test.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/test.pl	Tue Aug 19 13:00:53 2014 -0400
@@ -0,0 +1,55 @@
+#!/usr/bin/perl
+#V1.10
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $input_read1_file = $ARGV[0];
+my $input_read2_file = $ARGV[1];
+my $input_assembly_file = $ARGV[2];
+my $output_read1_file = $ARGV[3];
+my $output_read2_file = $ARGV[4];
+my $output_assembly_file = $ARGV[5];
+
+#$output_read1_file = $input_read1_file.".tmp";
+#$output_read2_file = $input_read2_file.".tmp";
+#$output_assembly_file = $input_assembly_file.".tmp";
+
+
+
+open(INR1, $input_read1_file) or die ("Can't open $input_read1_file\n");
+open(INR2, $input_read2_file) or die ("Can't open $input_read2_file\n");
+open(INAF, $input_assembly_file) or die ("Can't open $input_assembly_file\n");
+
+
+open(OUTR1, ">$output_read1_file") or die ("Can't open $output_read1_file\n");
+open(OUTR2, ">$output_read2_file") or die ("Can't open $output_read2_file\n");
+open(OUTAF, ">$output_assembly_file") or die ("Can't open $output_assembly_file\n");
+
+
+
+while (my $ligne = <INR1>){
+	print OUTR1 $ligne;
+}
+
+close (INR1);
+close (OUTR1);
+
+while (my $ligne = <INR2>){
+	print OUTR2 $ligne;
+}
+
+close (INR2);
+close (OUTR2);
+
+while (my $ligne = <INAF>){
+	print OUTAF $ligne;
+}
+
+close (INAF);
+close (OUTAF);
+
+print "Filler\n";
+print "$output_read1_file\n";
+
diff -r b7125d07b446 -r 658acc3202dc rapsodyn/test.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/test.xml	Tue Aug 19 13:00:53 2014 -0400
@@ -0,0 +1,21 @@
+<tool id="test" name="test" version="0.01">
+<description>Merge best results from Blast</description>
+<command interpreter="perl">
+    test.pl $input_read1_file $input_read2_file $input_assembly_file $output_read1_file $output_read2_file $output_assembly_file > $output_stat_file 
+</command>
+<inputs>
+<param name="input_read1_file"  type="data" format="fastq,fastqsolexa,fastqillumina,fastqsanger" label="Select a suitable input READ1 TRIMMED file from your history"/>
+<param name="input_read2_file"  type="data" format="fastq,fastqsolexa,fastqillumina,fastqsanger" label="Select a suitable input READ2 TRIMMED file from your history"/>
+<param name="input_assembly_file" type="data" format="fasta" label="Select a suitable input ASSEMBLY file from your history"/>
+</inputs>
+<outputs>
+ <data name="output_read1_file" format="fastqsanger" label="${tool.name} READ1 TRIMMED"/>
+ <data name="output_read2_file" format="fastqsanger" label="${tool.name} READ2 TRIMMED"/>
+ <data name="output_assembly_file" format="fasta" label="${tool.name} ASSEMBLY"/>
+ <data name="output_stat_file" format="txt" label="${tool.name} STATS"/>
+</outputs>
+
+<help>
+
+</help>
+</tool>
diff -r b7125d07b446 -r 658acc3202dc rapsodyn/tool_dependencies.xml
--- a/rapsodyn/tool_dependencies.xml	Thu Aug 14 09:39:11 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="sickle" version="1.210">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_sickle_1_210" owner="jjohnson" changeset_revision="a78ad39d5ede" />
-    </package>
-</tool_dependency>
-