diff Galaxy-Workflow-Detrprok_wf.ga @ 1:20e004d0292b draft default tip

Uploaded
author clairetn
date Mon, 20 May 2013 13:44:44 -0400
parents c265b11e7277
children
line wrap: on
line diff
--- a/Galaxy-Workflow-Detrprok_wf.ga	Mon Mar 25 05:51:08 2013 -0400
+++ b/Galaxy-Workflow-Detrprok_wf.ga	Mon May 20 13:44:44 2013 -0400
@@ -2,27 +2,27 @@
     "a_galaxy_workflow": "true", 
     "annotation": "", 
     "format-version": "0.1", 
-    "name": "Detrprok_current", 
+    "name": "Detrprok_wf", 
     "steps": {
         "0": {
-            "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
+            "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
             "id": 0, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
-                    "name": "positions list of all genome known annotations"
+                    "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
+                    "name": "genome annotations"
                 }
             ], 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 166, 
-                "top": 364
+                "left": 200, 
+                "top": 231.00001525878906
             }, 
             "tool_errors": null, 
             "tool_id": null, 
-            "tool_state": "{\"name\": \"positions list of all genome known annotations\"}", 
+            "tool_state": "{\"name\": \"genome annotations\"}", 
             "tool_version": null, 
             "type": "data_input", 
             "user_outputs": []
@@ -40,8 +40,8 @@
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 215, 
-                "top": 484
+                "left": 205, 
+                "top": 403.00001525878906
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -51,30 +51,43 @@
             "user_outputs": []
         }, 
         "2": {
-            "annotation": "", 
+            "annotation": "Select here the GFF file features that will be considered as initial annotations. Any term added here will cause pre-existing features with this term not to be predicted again by the workflow. Please use a comma separated list and use \"CDS\" rather than \"gene\" for protein coding genes. Suggested value: rRNA,tRNA,ncRNA,CDS", 
             "id": 2, 
             "input_connections": {
-                "inputFile": {
+                "formatType|inputFileName": {
                     "id": 0, 
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
-            "name": "clean Gff", 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool clean transcript file", 
+                    "name": "optionType"
+                }
+            ], 
+            "name": "clean transcript file", 
             "outputs": [
                 {
                     "name": "outputFile", 
-                    "type": "gff3"
+                    "type": "gtf"
                 }
             ], 
             "position": {
-                "left": 361, 
-                "top": 327
+                "left": 457, 
+                "top": 218.00001525878906
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "annotation selection"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/cleanGff/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"type\": \"\\\"tRNA,rRNA,ncRNA,CDS\\\"\", \"inputFile\": \"null\"}", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CleanTranscriptFile/1.0.0", 
+            "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"Yes\\\", \\\"value\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
@@ -97,13 +110,13 @@
                 }
             ], 
             "position": {
-                "left": 418, 
-                "top": 479
+                "left": 428, 
+                "top": 400.00001525878906
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutput1": {
                     "action_arguments": {
-                        "newname": "Read alignments in SAM format"
+                        "newname": "Read alignments (SAM format)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "output1"
@@ -111,13 +124,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "bam_to_sam", 
-            "tool_state": "{\"header\": \"\\\"False\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_state": "{\"header\": \"\\\"True\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
             "tool_version": "1.0.3", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "4": {
-            "annotation": "Clusters annotated proximal genes into operons. \nParameter to be set: op_gap. \nGenes separated by a gap smaller than op_gap are clustered \n(suggested value: 10 to 150).", 
+            "annotation": "Clusters annotated proximal genes into operons. Parameter to be set: op_gap. Genes separated by a gap smaller than op_gap are clustered (suggested value: 10 to 150).", 
             "id": 4, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -127,29 +140,25 @@
             }, 
             "inputs": [
                 {
-                    "description": "runtime parameter for tool Clusterize", 
+                    "description": "runtime parameter for tool clusterize", 
                     "name": "distance"
                 }
             ], 
-            "name": "Clusterize", 
+            "name": "clusterize", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
                     "type": "gff3"
-                }, 
-                {
-                    "name": "outputFileLog", 
-                    "type": "txt"
                 }
             ], 
             "position": {
-                "left": 547, 
-                "top": 297
+                "left": 700, 
+                "top": 200.00001525878906
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "Annotation with \"operon\""
+                        "newname": "Annotation with operon-like features"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
@@ -157,13 +166,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
-            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}", 
+            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "5": {
-            "annotation": "Clusters overlapping or proximal reads to produce read clusters. \nParameter to be set: clust_gap. \nReads separated by a gap smaller than \nclust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart).", 
+            "annotation": "Clusters overlapping or proximal reads to produce read clusters. Parameter to be set: clust_gap. Reads separated by a gap smaller than clust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart)", 
             "id": 5, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -173,29 +182,25 @@
             }, 
             "inputs": [
                 {
-                    "description": "runtime parameter for tool Clusterize", 
+                    "description": "runtime parameter for tool clusterize", 
                     "name": "distance"
                 }
             ], 
-            "name": "Clusterize", 
+            "name": "clusterize", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
                     "type": "gff3"
-                }, 
-                {
-                    "name": "outputFileLog", 
-                    "type": "txt"
                 }
             ], 
             "position": {
-                "left": 496, 
-                "top": 596
+                "left": 662, 
+                "top": 505.00001525878906
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "Read clusters"
+                        "newname": "Read clusters (with exon)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
@@ -203,31 +208,96 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
-            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 5, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "6": {
-            "annotation": "Selects read clusters that overlap annotations in the same direction. \nParameter to be set: RNA_gap.\nA read cluster separated from an annotation by a gap smaller than RNA_gap is selected (suggested value: 25).", 
+            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", 
             "id": 6, 
             "input_connections": {
-                "formatType2|inputFileName2": {
+                "inputFile": {
                     "id": 4, 
                     "output_name": "outputFileGff"
-                }, 
-                "formatType|inputFileName1": {
+                }
+            }, 
+            "inputs": [], 
+            "name": "remove exon lines", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 892, 
+                "top": 221.00001525878906
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "Annotation with operon-like (without exon)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", 
+            "id": 7, 
+            "input_connections": {
+                "inputFile": {
                     "id": 5, 
                     "output_name": "outputFileGff"
                 }
             }, 
-            "inputs": [
+            "inputs": [], 
+            "name": "remove exon lines", 
+            "outputs": [
                 {
-                    "description": "runtime parameter for tool Compare Overlapping Small Query", 
-                    "name": "OptionDistance"
+                    "name": "outputFile", 
+                    "type": "gff3"
                 }
             ], 
-            "name": "Compare Overlapping Small Query", 
+            "position": {
+                "left": 892, 
+                "top": 505.00001525878906
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "Read clusters"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "Technical step: orders the features by increasing positions.", 
+            "id": 8, 
+            "input_connections": {
+                "formatType|inputFileName": {
+                    "id": 6, 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "collapse reads", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
@@ -235,8 +305,100 @@
                 }
             ], 
             "position": {
-                "left": 659, 
-                "top": 417
+                "left": 1072, 
+                "top": 261.00001525878906
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFileGff": {
+                    "action_arguments": {
+                        "newname": "Annotation list with operon-like feature"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "Selects read clusters that form new independent annotations. Parameter to be set: RNA_gap. Read clusters at a distance from existing annotations larger than RNA_gap are selected (suggested value: 25).", 
+            "id": 9, 
+            "input_connections": {
+                "formatType2|inputFileName2": {
+                    "id": 8, 
+                    "output_name": "outputFileGff"
+                }, 
+                "formatType|inputFileName1": {
+                    "id": 7, 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool compare overlapping small query", 
+                    "name": "OptionDistance"
+                }
+            ], 
+            "name": "compare overlapping small query", 
+            "outputs": [
+                {
+                    "name": "outputFileGff", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 1197, 
+                "top": 521.0000152587891
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFileGff": {
+                    "action_arguments": {
+                        "newname": "Read clusters not overlapping annotation"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
+            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "Selects read clusters that overlap annotations in the same direction. Parameter to be set: RNA_gap. A read cluster separated from an annotation by a gap smaller than RNA_gap is selected. Caution: use same RNA_gap value as in previous step!", 
+            "id": 10, 
+            "input_connections": {
+                "formatType2|inputFileName2": {
+                    "id": 8, 
+                    "output_name": "outputFileGff"
+                }, 
+                "formatType|inputFileName1": {
+                    "id": 7, 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool compare overlapping small query", 
+                    "name": "OptionDistance"
+                }
+            ], 
+            "name": "compare overlapping small query", 
+            "outputs": [
+                {
+                    "name": "outputFileGff", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 1407, 
+                "top": 328.00001525878906
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
@@ -249,31 +411,26 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
-            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
+            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "7": {
-            "annotation": "Selects read clusters that form new independent annotations. \nParameter to be set: RNA_gap.\nRead clusters at a distance from existing annotations larger than RNA_gap are selected. Caution: use same RNA_gap value as in previous step!", 
-            "id": 7, 
+        "11": {
+            "annotation": "Selection of read clusters that are antisense of an extended annotation. This step produces a first list of antisense candidates.", 
+            "id": 11, 
             "input_connections": {
                 "formatType2|inputFileName2": {
-                    "id": 4, 
+                    "id": 8, 
                     "output_name": "outputFileGff"
                 }, 
                 "formatType|inputFileName1": {
-                    "id": 5, 
+                    "id": 9, 
                     "output_name": "outputFileGff"
                 }
             }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Compare Overlapping Small Query", 
-                    "name": "OptionDistance"
-                }
-            ], 
-            "name": "Compare Overlapping Small Query", 
+            "inputs": [], 
+            "name": "compare overlapping small query", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
@@ -281,13 +438,13 @@
                 }
             ], 
             "position": {
-                "left": 742, 
-                "top": 588
+                "left": 1660, 
+                "top": 531.0000152587891
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "Read clusters not overlapping annotation"
+                        "newname": "first list of asRNA"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
@@ -295,21 +452,62 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
-            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
+            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "8": {
+        "12": {
+            "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation. This step produces a first list of small RNAs.", 
+            "id": 12, 
+            "input_connections": {
+                "formatType2|inputFileName2": {
+                    "id": 8, 
+                    "output_name": "outputFileGff"
+                }, 
+                "formatType|inputFileName1": {
+                    "id": 9, 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "inputs": [], 
+            "name": "compare overlapping small query", 
+            "outputs": [
+                {
+                    "name": "outputFileGff", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 1665, 
+                "top": 673
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFileGff": {
+                    "action_arguments": {
+                        "newname": "first list of sRNA"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
+            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
             "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.", 
-            "id": 8, 
+            "id": 13, 
             "input_connections": {
                 "input1": {
-                    "id": 4, 
+                    "id": 8, 
                     "output_name": "outputFileGff"
                 }, 
                 "queries_0|input2": {
-                    "id": 6, 
+                    "id": 10, 
                     "output_name": "outputFileGff"
                 }
             }, 
@@ -322,8 +520,8 @@
                 }
             ], 
             "position": {
-                "left": 819, 
-                "top": 294
+                "left": 1725, 
+                "top": 228.00001525878906
             }, 
             "post_job_actions": {
                 "RenameDatasetActionout_file1": {
@@ -336,105 +534,27 @@
             }, 
             "tool_errors": null, 
             "tool_id": "cat1", 
-            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "9": {
-            "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. \nParameter to be set: RNA_gap.\nRead cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!", 
-            "id": 9, 
+        "14": {
+            "annotation": "Filters antisense RNAs based on their size. Parameter to be set: as_min_size. as_min_size is the minimal size for calling an antisense RNA (suggestion: 50).", 
+            "id": 14, 
             "input_connections": {
                 "formatType|inputFileName": {
-                    "id": 8, 
-                    "output_name": "out_file1"
+                    "id": 11, 
+                    "output_name": "outputFileGff"
                 }
             }, 
             "inputs": [
                 {
-                    "description": "runtime parameter for tool Clusterize", 
-                    "name": "distance"
-                }
-            ], 
-            "name": "Clusterize", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }, 
-                {
-                    "name": "outputFileLog", 
-                    "type": "txt"
+                    "description": "runtime parameter for tool restrict from size", 
+                    "name": "OptionMin"
                 }
             ], 
-            "position": {
-                "left": 1036, 
-                "top": 307
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "Extended annotation"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
-            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "10": {
-            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", 
-            "id": 10, 
-            "input_connections": {
-                "input": {
-                    "id": 9, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Select", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 1232, 
-                "top": 319
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionout_file1": {
-                    "action_arguments": {
-                        "newname": "Extended annotation without \"exon\" lines"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Grep1", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "11": {
-            "annotation": "Technical step: orders extended annotations by positions.", 
-            "id": 11, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 10, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [], 
-            "name": "collapse reads", 
+            "name": "restrict from size", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
@@ -442,81 +562,41 @@
                 }
             ], 
             "position": {
-                "left": 973, 
-                "top": 460
+                "left": 1959.2166748046875, 
+                "top": 548.4833526611328
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "Ordrered and extended annotation"
+                        "newname": "asRNA list modified (filtered on their size)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
+            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "12": {
-            "annotation": "Splits extended annotations into UTRs, CDS and/or operon spacers.", 
-            "id": 12, 
+        "15": {
+            "annotation": "Filters small RNAs based on their size. Parameter to be set: sRNA_min_size. sRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).", 
+            "id": 15, 
             "input_connections": {
-                "referenciesFile": {
-                    "id": 4, 
-                    "output_name": "outputFileGff"
-                }, 
-                "transcriptsFile": {
-                    "id": 11, 
+                "formatType|inputFileName": {
+                    "id": 12, 
                     "output_name": "outputFileGff"
                 }
             }, 
-            "inputs": [], 
-            "name": "splitTranscriptGff", 
-            "outputs": [
+            "inputs": [
                 {
-                    "name": "outputFile", 
-                    "type": "gff3"
+                    "description": "runtime parameter for tool restrict from size", 
+                    "name": "OptionMin"
                 }
             ], 
-            "position": {
-                "left": 1221, 
-                "top": 456
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFile": {
-                    "action_arguments": {
-                        "newname": "UTRs, CDSs and/or operons"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/splitTranscriptGff/1.0.0", 
-            "tool_state": "{\"transcriptsFile\": \"null\", \"__page__\": 0, \"referenciesFile\": \"null\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "13": {
-            "annotation": "Selection of read clusters that are antisense of an extended annotation. \nThis step produces a first list of antisense candidates.", 
-            "id": 13, 
-            "input_connections": {
-                "formatType2|inputFileName2": {
-                    "id": 11, 
-                    "output_name": "outputFileGff"
-                }, 
-                "formatType|inputFileName1": {
-                    "id": 7, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Compare Overlapping Small Query", 
+            "name": "restrict from size", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
@@ -524,40 +604,41 @@
                 }
             ], 
             "position": {
-                "left": 1155, 
-                "top": 617
+                "left": 1954, 
+                "top": 683
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "first list of asRNA"
+                        "newname": "sRNA list modified (filtered on their size)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
-            "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
+            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "14": {
-            "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation.\nThis step produces a first list of small RNAs.", 
-            "id": 14, 
+        "16": {
+            "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. Parameter to be set: RNA_gap. Read cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!", 
+            "id": 16, 
             "input_connections": {
-                "formatType2|inputFileName2": {
-                    "id": 11, 
-                    "output_name": "outputFileGff"
-                }, 
-                "formatType|inputFileName1": {
-                    "id": 7, 
-                    "output_name": "outputFileGff"
+                "formatType|inputFileName": {
+                    "id": 13, 
+                    "output_name": "out_file1"
                 }
             }, 
-            "inputs": [], 
-            "name": "Compare Overlapping Small Query", 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool clusterize", 
+                    "name": "distance"
+                }
+            ], 
+            "name": "clusterize", 
             "outputs": [
                 {
                     "name": "outputFileGff", 
@@ -565,110 +646,27 @@
                 }
             ], 
             "position": {
-                "left": 1068, 
-                "top": 766
+                "left": 1963, 
+                "top": 257.00001525878906
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "first list of sRNA"
+                        "newname": "Extended annotation (with exon)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
-            "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "15": {
-            "annotation": "Counts reads overlapping UTRs, CDSs and/or operon spacers in order to compute read coverage (with a minimal overlapping region of 10 nt between read and genetic element). Output file of this step can be used to obtain read coverage of 5'UTRs, 3'UTRs, CDSs, or operon spacers.", 
-            "id": 15, 
-            "input_connections": {
-                "formatType2|inputFileName2": {
-                    "id": 3, 
-                    "output_name": "output1"
-                }, 
-                "formatType|inputFileName1": {
-                    "id": 12, 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Compare Overlapping Small Reference", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 1417, 
-                "top": 506
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "UTRs, CDSs and operons (with the number of overlapping reads)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallRef/1.0.0", 
-            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"sam\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 4}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"10\\\"}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "16": {
-            "annotation": "Filters antisense RNA candidates based on their number of overlapping reads.\nParameter to be set: as_min_reads.\nAntisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).", 
-            "id": 16, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 13, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool select by tag", 
-                    "name": "OptionMin"
-                }
-            ], 
-            "name": "select by tag", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 1461, 
-                "top": 663
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "asRNA list modified (filtered on their number of overlapping reads)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
+            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "17": {
-            "annotation": "Filters sRNA candidates based on their number of overlapping reads.\nParameter to be set: sRNA_min_reads.\nSmall RNAs with a number of reads higher than sRNA_min_reads are selected (suggested value: 12).", 
+            "annotation": "Filters antisense RNA candidates based on their number of overlapping reads. Parameter to be set: as_min_reads. Antisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).", 
             "id": 17, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -690,13 +688,13 @@
                 }
             ], 
             "position": {
-                "left": 1389, 
-                "top": 794
+                "left": 2162.2166748046875, 
+                "top": 554.4833526611328
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "sRNA list modified (filtered on their number of overlapping reads)"
+                        "newname": "asRNA list modified (filtered on their number of overlapping reads)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
@@ -704,13 +702,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 2, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "18": {
-            "annotation": "Technical step: coverage computation needs \"nbElements\" tag in place of \"nbOverlaps\".", 
+            "annotation": "Filters sRNA candidates based on their number of overlapping reads. Parameter to be set: sRNA_min_reads. Small RNAs with a number of reads higher than sRNA_min_reads are selected (suggested value: 12).", 
             "id": 18, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -718,367 +716,6 @@
                     "output_name": "outputFileGff"
                 }
             }, 
-            "inputs": [], 
-            "name": "change tag name", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 1696, 
-                "top": 541
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "long 5'UTR list modified (tag \"nbElements\")"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"Tag\": \"\\\"nbOverlaps\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"name\": \"\\\"nbElements\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "19": {
-            "annotation": "Clusters proximal antisense RNAs in the same direction.\nParameter to be set: RNA_merge.\nAntisense RNAs located less than RNA_merge apart are merged (suggestion: 50).", 
-            "id": 19, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 16, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Clusterize", 
-                    "name": "distance"
-                }
-            ], 
-            "name": "Clusterize", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }, 
-                {
-                    "name": "outputFileLog", 
-                    "type": "txt"
-                }
-            ], 
-            "position": {
-                "left": 1658, 
-                "top": 660
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "asRNA list modified (asRNA clusters)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
-            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "20": {
-            "annotation": "Clusters proximal small RNAs in the same direction.\nParameter to be set: RNA_merge.\nSmall RNAs located less than RNA_merge apart are merged (suggestion: 50).", 
-            "id": 20, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 17, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Clusterize", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }, 
-                {
-                    "name": "outputFileLog", 
-                    "type": "txt"
-                }
-            ], 
-            "position": {
-                "left": 1602, 
-                "top": 797
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "sRNA list modified (sRNA clusters)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
-            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"\\\"50\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "21": {
-            "annotation": "Technical step: extracts 5'UTR features for following steps.", 
-            "id": 21, 
-            "input_connections": {
-                "input1": {
-                    "id": 18, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Extract features", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 1917, 
-                "top": 547
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionout_file1": {
-                    "action_arguments": {
-                        "newname": "first list of long 5'UTR"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Extract_features1", 
-            "tool_state": "{\"column_choice\": \"{\\\"col\\\": \\\"2\\\", \\\"__current_case__\\\": 2, \\\"feature\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"utr5\\\"]}}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "22": {
-            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", 
-            "id": 22, 
-            "input_connections": {
-                "input": {
-                    "id": 19, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Select", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 1859, 
-                "top": 682
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionout_file1": {
-                    "action_arguments": {
-                        "newname": "asRNA list modified (without \"exon\" lines)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Grep1", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"pattern\": \"\\\"exon\\\"\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "23": {
-            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", 
-            "id": 23, 
-            "input_connections": {
-                "input": {
-                    "id": 20, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Select", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 1804, 
-                "top": 813
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionout_file1": {
-                    "action_arguments": {
-                        "newname": "sRNA list modified (without \"exon\" lines)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Grep1", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "24": {
-            "annotation": "Filters 5'UTR based on their size.\nParameter to be set: 5UTR_min_size.\n5'UTRs larger than 5UTR_min_size are selected (suggestion value: 50).", 
-            "id": 24, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 21, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool restrict from size", 
-                    "name": "OptionMin"
-                }
-            ], 
-            "name": "restrict from size", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 2132, 
-                "top": 570
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "long 5'UTR list modified (filtered on their size)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
-            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "25": {
-            "annotation": "Filters antisense RNAs based on their size.\nParameter to be set: as_min_size.\nas_min_size is the minimal size for calling an antisense RNA (suggestion: 50).", 
-            "id": 25, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 22, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool restrict from size", 
-                    "name": "OptionMin"
-                }
-            ], 
-            "name": "restrict from size", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 2085, 
-                "top": 691
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "asRNA list modified (filtered on their size)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
-            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "26": {
-            "annotation": "Filters small RNAs based on their size.\nParameter to be set: sRNA_min_size.\nsRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).", 
-            "id": 26, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 23, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool restrict from size", 
-                    "name": "OptionMin"
-                }
-            ], 
-            "name": "restrict from size", 
-            "outputs": [
-                {
-                    "name": "outputFileGff", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 2017, 
-                "top": 824
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFileGff": {
-                    "action_arguments": {
-                        "newname": "sRNA list modified (filtered on their size)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
-            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "27": {
-            "annotation": "Filters long 5' UTR candidates based on their number of overlapping reads.\nParameter to be set: 5UTR_min_reads.\nLong 5'UTR with a number of reads higher than 5UTR_min_reads is selected (suggested value: 10).", 
-            "id": 27, 
-            "input_connections": {
-                "formatType|inputFileName": {
-                    "id": 24, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
             "inputs": [
                 {
                     "description": "runtime parameter for tool select by tag", 
@@ -1093,13 +730,13 @@
                 }
             ], 
             "position": {
-                "left": 2344, 
-                "top": 577
+                "left": 2168, 
+                "top": 687
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFileGff": {
                     "action_arguments": {
-                        "newname": "long 5'UTR list modified (filtered on their number of overlapping reads)"
+                        "newname": "sRNA list modified (filtered on their number of overlapping reads)"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFileGff"
@@ -1107,20 +744,519 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 2, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", 
+            "id": 19, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 16, 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "inputs": [], 
+            "name": "remove exon lines", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 2176, 
+                "top": 274.00001525878906
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "Extended annotation"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "20": {
+            "annotation": "Clusters proximal antisense RNAs in the same direction. Parameter to be set: RNA_merge. Antisense RNAs located less than RNA_merge apart are merged (suggestion: 50).", 
+            "id": 20, 
+            "input_connections": {
+                "formatType|inputFileName": {
+                    "id": 17, 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool clusterize", 
+                    "name": "distance"
+                }
+            ], 
+            "name": "clusterize", 
+            "outputs": [
+                {
+                    "name": "outputFileGff", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 2395.38330078125, 
+                "top": 567.8166809082031
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFileGff": {
+                    "action_arguments": {
+                        "newname": "asRNA list modified (asRNA clusters)"
+                    }, 
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@@ -1130,31 +1266,374 @@
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+            "post_job_actions": {
+                "RenameDatasetActionout_file1": {
+                    "action_arguments": {
+                        "newname": "5 prime extension"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "Extract_features1", 
+            "tool_state": "{\"column_choice\": \"{\\\"col\\\": \\\"2\\\", \\\"__current_case__\\\": 2, \\\"feature\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"utr5\\\"]}}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "37": {
+            "annotation": "Technical step: change feature name from operon to operon_spacer", 
+            "id": 37, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 34, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "change GFF features", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gff"
+                }
+            ], 
+            "position": {
+                "left": 3686, 
+                "top": 387.53334045410156
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+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "operon_spacer list"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"operon\\\"\", \"outputFeature\": \"\\\"operon_spacer\\\"\", \"inputFile\": \"null\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "29": {
-            "annotation": "Uses an RGB color tag for visualization of small RNAs in the Artemis environment.", 
-            "id": 29, 
+        "38": {
+            "annotation": "Technical step: change feature name from urt3 to 3_extension", 
+            "id": 38, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 35, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "change GFF features", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gff"
+                }
+            ], 
+            "position": {
+                "left": 3682, 
+                "top": 481.53334045410156
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+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "3_extension list"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"utr3\\\"\", \"outputFeature\": \"\\\"3_extension\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "39": {
+            "annotation": "Technical step: change feature name from urt5 to 5_extension", 
+            "id": 39, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 36, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "change GFF features", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gff"
+                }
+            ], 
+            "position": {
+                "left": 3640, 
+                "top": 575.5333404541016
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFile": {
+                    "action_arguments": {
+                        "newname": "all 5_extensions list"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"utr5\\\"\", \"outputFeature\": \"\\\"5_extension\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "40": {
+            "annotation": "Filters 5' extensions based on their size. Parameter to be set: 5_extension_min_size. 5' extensions larger than 5_extension_min_size are selected (suggestion value: 50).", 
+            "id": 40, 
+            "input_connections": {
+                "formatType|inputFileName": {
+                    "id": 39, 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool restrict from size", 
+                    "name": "OptionMin"
+                }
+            ], 
+            "name": "restrict from size", 
+            "outputs": [
+                {
+                    "name": "outputFileGff", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 3823, 
+                "top": 580.0000152587891
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFileGff": {
+                    "action_arguments": {
+                        "newname": "long 5_extensions list modified (filtered on their size)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", 
+            "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "41": {
+            "annotation": "Filters long 5 prime extension candidates based on their number of overlapping reads. Parameter to be set: 5_extension_min_reads. Long 5 prime extensions with a number of reads higher than 5_extension_min_reads are selected (suggested value: 10).", 
+            "id": 41, 
+            "input_connections": {
+                "formatType|inputFileName": {
+                    "id": 40, 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool select by tag", 
+                    "name": "OptionMin"
+                }
+            ], 
+            "name": "select by tag", 
+            "outputs": [
+                {
+                    "name": "outputFileGff", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 3997, 
+                "top": 586.0000152587891
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutputFileGff": {
+                    "action_arguments": {
+                        "newname": "long 5_extensions list modified (filtered on their number of overlapping reads)"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputFileGff"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 2, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbOverlappingReads\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "42": {
+            "annotation": "Uses an RGB color tag for visualization of long 5_extension in the Artemis environment.", 
+            "id": 42, 
             "input_connections": {
                 "referenciesFile": {
-                    "id": 26, 
+                    "id": 41, 
                     "output_name": "outputFileGff"
                 }
             }, 
@@ -1167,132 +1646,21 @@
                 }
             ], 
             "position": {
-                "left": 2247, 
-                "top": 838
+                "left": 4176, 
+                "top": 591.0000152587891
             }, 
             "post_job_actions": {
                 "RenameDatasetActionoutputFile": {
                     "action_arguments": {
-                        "newname": "sRNA list modified (annotation color)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"250 128 114\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "30": {
-            "annotation": "Uses an RGB color tag for visualization of long 5' UTRs in the Artemis environment.", 
-            "id": 30, 
-            "input_connections": {
-                "referenciesFile": {
-                    "id": 27, 
-                    "output_name": "outputFileGff"
-                }
-            }, 
-            "inputs": [], 
-            "name": "colorGff", 
-            "outputs": [
-                {
-                    "name": "outputFile", 
-                    "type": "gff"
-                }
-            ], 
-            "position": {
-                "left": 2525, 
-                "top": 610
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFile": {
-                    "action_arguments": {
-                        "newname": "final long 5'UTR list (with the annotation color)"
+                        "newname": "long 5_extensions list"
                     }, 
                     "action_type": "RenameDatasetAction", 
                     "output_name": "outputFile"
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"255 105 180\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "31": {
-            "annotation": "Technical step: changes \"transcript\" for \"asRNA\" in the 3rd column.", 
-            "id": 31, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 28, 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "change gff Features", 
-            "outputs": [
-                {
-                    "name": "outputFile", 
-                    "type": "gff"
-                }
-            ], 
-            "position": {
-                "left": 2542, 
-                "top": 727
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFile": {
-                    "action_arguments": {
-                        "newname": "final asRNA list (with the annotation color)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"transcript\\\"\", \"outputFeature\": \"\\\"asRNA\\\"\", \"inputFile\": \"null\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "32": {
-            "annotation": "Technical step: changes \"transcript\" for \"sRNA\" in the 3rd column.", 
-            "id": 32, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 29, 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "change gff Features", 
-            "outputs": [
-                {
-                    "name": "outputFile", 
-                    "type": "gff"
-                }
-            ], 
-            "position": {
-                "left": 2464, 
-                "top": 827
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputFile": {
-                    "action_arguments": {
-                        "newname": "final sRNA list (with the annotation color)"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"transcript\\\"\", \"outputFeature\": \"\\\"sRNA\\\"\", \"inputFile\": \"null\"}", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"255 105 180\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []