changeset 7:158f0fdfd552 draft

Uploaded

--- a/Galaxy-Workflow-_DetR_Prok_v3__.ga	Fri Mar 08 12:57:22 2013 -0500
+++ b/Galaxy-Workflow-_DetR_Prok_v3__.ga	Wed Mar 20 10:06:30 2013 -0400
@@ -5,20 +5,20 @@
     "name": "\"DetR'Prok_v3''", 
     "steps": {
         "0": {
-            "annotation": "The annotations file you have to import here concerns the coding genes, tRNA, rRNA, and all already known ncRNA. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution that the 1srt column has exactly the same identifier than the genome sequence used for reads 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. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
             "id": 0, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "The annotations file you have to import here concerns the coding genes, tRNA, rRNA, and all already known ncRNA. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution that the 1srt column has exactly the same identifier than the genome sequence used for reads mapping.", 
+                    "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"
                 }
             ], 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 160.8999786376953, 
-                "top": 337.28334045410156
+                "left": 160.9000244140625, 
+                "top": 353.75
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -28,20 +28,20 @@
             "user_outputs": []
         }, 
         "1": {
-            "annotation": "Here you have to import a resulting bam file coming from an alignment, or mapping, of reads on the genome sequence. \nYou may use bowtie (or another mapper) to realise this mapping step (keep only unique map).", 
+            "annotation": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", 
             "id": 1, 
             "input_connections": {}, 
             "inputs": [
                 {
-                    "description": "Here you have to import a resulting bam file coming from an alignment, or mapping, of reads on the genome sequence. \nYou may use bowtie (or another mapper) to realise this mapping step (keep only unique map).", 
+                    "description": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", 
                     "name": "read alignments on genome"
                 }
             ], 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 209.8999786376953, 
-                "top": 464.5166778564453
+                "left": 215.9000244140625, 
+                "top": 484.9833526611328
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -68,8 +68,8 @@
                 }
             ], 
             "position": {
-                "left": 361.1166534423828, 
-                "top": 310.6166687011719
+                "left": 361.11669921875, 
+                "top": 327.0833282470703
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -97,8 +97,8 @@
                 }
             ], 
             "position": {
-                "left": 418.66664123535156, 
-                "top": 463.5166778564453
+                "left": 418.666748046875, 
+                "top": 479.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -109,7 +109,7 @@
             "user_outputs": []
         }, 
         "4": {
-            "annotation": "In box specify the maximal intergenique distance to define operon. This distance depends on the gene density of the organism (ex. 30 for Escherichia coli, 150 for Vibrio splendidus)", 
+            "annotation": "In box, enter the maximal intergenic distance used for operon definition. This distance depends on the gene density of the organism (try 30 for Escherichia coli, 150 for Vibrio splendidus).", 
             "id": 4, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -135,8 +135,8 @@
                 }
             ], 
             "position": {
-                "left": 540.0166473388672, 
-                "top": 275.23333740234375
+                "left": 547.0167236328125, 
+                "top": 297.6999969482422
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -147,7 +147,7 @@
             "user_outputs": []
         }, 
         "5": {
-            "annotation": "Association of collinear overlapping reads giving read clusters.", 
+            "annotation": "Clusters overlaping reads of same direction to produce read clusters.", 
             "id": 5, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -155,7 +155,12 @@
                     "output_name": "output1"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Clusterize", 
+                    "name": "distance"
+                }
+            ], 
             "name": "Clusterize", 
             "outputs": [
                 {
@@ -168,19 +173,19 @@
                 }
             ], 
             "position": {
-                "left": 496.4333190917969, 
-                "top": 580.5166778564453
+                "left": 496.433349609375, 
+                "top": 596.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
-            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"\\\"0\\\"\", \"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\\\"\", \"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_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
         "6": {
-            "annotation": "Selection of read clusters that overlap the annotations (collinear stackings). In box, specify a maximal distance to associate read clusters with annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are distants of 15 nt).", 
+            "annotation": "Selects read clusters that overlap annotations in the same direction. In box, enter maximal distance to associate a cluster to an annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are 15-nt apart).", 
             "id": 6, 
             "input_connections": {
                 "formatType2|inputFileName2": {
@@ -206,8 +211,8 @@
                 }
             ], 
             "position": {
-                "left": 655.1999816894531, 
-                "top": 417.5166778564453
+                "left": 655.2000732421875, 
+                "top": 433.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -218,7 +223,7 @@
             "user_outputs": []
         }, 
         "7": {
-            "annotation": "Selection of read clusters that are outside of the annotations (collinear stackings and invert selection).  In box, specify th same maximal distance to associate read clusters with annotation than the previous step (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are distants of 15 nt).", 
+            "annotation": "Selects read clusters that form new independent annotations. In box, enter minimal distance between cluster and existing annotations. Caution: use same value as in previous step!", 
             "id": 7, 
             "input_connections": {
                 "formatType2|inputFileName2": {
@@ -244,8 +249,8 @@
                 }
             ], 
             "position": {
-                "left": 742.1999816894531, 
-                "top": 572.2833404541016
+                "left": 742.2000732421875, 
+                "top": 588.7500152587891
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -256,7 +261,7 @@
             "user_outputs": []
         }, 
         "8": {
-            "annotation": "Technical step: fusing of two files, annotations and read clusters that overlap annotation, in order to define transcription units by clustering them.", 
+            "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be use to define transcription units.", 
             "id": 8, 
             "input_connections": {
                 "input1": {
@@ -277,8 +282,8 @@
                 }
             ], 
             "position": {
-                "left": 819.9666442871094, 
-                "top": 278.5166778564453
+                "left": 819.9666748046875, 
+                "top": 294.98333740234375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -289,7 +294,7 @@
             "user_outputs": []
         }, 
         "9": {
-            "annotation": "Collinear clustering of annotations and read clusters that overlap them. In box specify the same maximal distance than you gave in previous steps (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are distants of 15 nt). This step defines transcription units.", 
+            "annotation": "Selects read clusters that overlap annotations in the same direction. In box, enter maximal distance to associate a cluster to an annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are 15-nt apart). This step defines transcription units.", 
             "id": 9, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -315,8 +320,8 @@
                 }
             ], 
             "position": {
-                "left": 1036.7333374023438, 
-                "top": 291.5166778564453
+                "left": 1036.7333984375, 
+                "top": 307.98333740234375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -327,7 +332,7 @@
             "user_outputs": []
         }, 
         "10": {
-            "annotation": "Technical step: suppress \"exon\" features created by the use of the distance option in the previous clustering step.", 
+            "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": {
@@ -344,8 +349,8 @@
                 }
             ], 
             "position": {
-                "left": 1232.5, 
-                "top": 303.5166778564453
+                "left": 1232.5000610351562, 
+                "top": 319.98333740234375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -356,7 +361,7 @@
             "user_outputs": []
         }, 
         "11": {
-            "annotation": "List of transcription units (ordered by increasing positions).", 
+            "annotation": "List of transcription units (ordered by positions).", 
             "id": 11, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -373,8 +378,8 @@
                 }
             ], 
             "position": {
-                "left": 973.2666625976562, 
-                "top": 444.5166778564453
+                "left": 973.2667236328125, 
+                "top": 460.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -385,7 +390,7 @@
             "user_outputs": []
         }, 
         "12": {
-            "annotation": "Split transcription units in UTRs, CDS and/or operon spacers.", 
+            "annotation": "Splits transcription units into UTRs, CDS and/or operon spacers.", 
             "id": 12, 
             "input_connections": {
                 "referenciesFile": {
@@ -406,8 +411,8 @@
                 }
             ], 
             "position": {
-                "left": 1215.2833251953125, 
-                "top": 435.5500030517578
+                "left": 1215.2833862304688, 
+                "top": 452.0166778564453
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -418,7 +423,7 @@
             "user_outputs": []
         }, 
         "13": {
-            "annotation": "Selection of read clusters that are outside and not in antisense of the annotations (complementary  selection, \"invert match\", of an antisense stackings of read clusters and annotations ; use a strict inclusion by indicating that 100% of the query must overlap). This step constitute the fisrt list of small ncRNA.", 
+            "annotation": "Selection of read clusters that are outside and not in antisense of transcription units. This step produces the first list of small RNAs.", 
             "id": 13, 
             "input_connections": {
                 "formatType2|inputFileName2": {
@@ -439,8 +444,8 @@
                 }
             ], 
             "position": {
-                "left": 1068.0333251953125, 
-                "top": 750.0500030517578
+                "left": 1068.0333862304688, 
+                "top": 766.5166778564453
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -451,7 +456,7 @@
             "user_outputs": []
         }, 
         "14": {
-            "annotation": "Selection of read clusters that are both outside and in antisense of the annotations (antisense stackings of read clusters and annotations ; use a strict inclusion by indicating that 100% of the query must overlap).", 
+            "annotation": "Selection of read clusters that are antisense of the transcription units.", 
             "id": 14, 
             "input_connections": {
                 "formatType2|inputFileName2": {
@@ -472,8 +477,8 @@
                 }
             ], 
             "position": {
-                "left": 1170.0333251953125, 
-                "top": 602.2833404541016
+                "left": 1170.0333862304688, 
+                "top": 618.7500152587891
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -484,7 +489,7 @@
             "user_outputs": []
         }, 
         "15": {
-            "annotation": "Collinear crossing of reads with UTRs, CDS and/or operon spacers in order to compute their read coverage (with a minimal overlapping region of 10 nt between read and genetic element). \nAiming at caracterize ncRNA, this workflow will next only focuses on 5'UTR, but you may use the output file of this step in order to exploit the read coverage of other elements like 3'UTR, CDS, or operon spacers.", 
+            "annotation": "Count 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": {
@@ -505,8 +510,8 @@
                 }
             ], 
             "position": {
-                "left": 1417.7999877929688, 
-                "top": 498.5166778564453
+                "left": 1417.800048828125, 
+                "top": 514.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -517,7 +522,7 @@
             "user_outputs": []
         }, 
         "16": {
-            "annotation": "Number of overlapping reads filter: keep only small ncRNA with the number of overlapping reads or more you want (ex. specify 10 in the input box).", 
+            "annotation": "Enter in box the minimum number of reads for calling an sRNA (suggested: 10).", 
             "id": 16, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -539,8 +544,8 @@
                 }
             ], 
             "position": {
-                "left": 1389.0999145507812, 
-                "top": 778.0500030517578
+                "left": 1389.1000366210938, 
+                "top": 794.5166778564453
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -551,7 +556,7 @@
             "user_outputs": []
         }, 
         "17": {
-            "annotation": "Number of overlapping reads filter: keep only antisense expression with the number of overlapping reads or more you want (ex. specify 5 in the input box).", 
+            "annotation": "Enter in box the minimum number of reads for calling an antisense RNA (suggested: 10).", 
             "id": 17, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -573,8 +578,8 @@
                 }
             ], 
             "position": {
-                "left": 1461.3333129882812, 
-                "top": 647.2833404541016
+                "left": 1461.3333740234375, 
+                "top": 663.7500152587891
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -585,7 +590,7 @@
             "user_outputs": []
         }, 
         "18": {
-            "annotation": "Technical step: coverage computation need a \"nbElements\" tag in place of the \"nbOverlaps\" one.", 
+            "annotation": "Technical step: coverage computation needs \"nbElements\" tag in place of \"nbOverlaps\".", 
             "id": 18, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -602,8 +607,8 @@
                 }
             ], 
             "position": {
-                "left": 1696.6166381835938, 
-                "top": 524.7500152587891
+                "left": 1696.61669921875, 
+                "top": 541.2166595458984
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -614,7 +619,7 @@
             "user_outputs": []
         }, 
         "19": {
-            "annotation": "Association of close small RNA (use a maximal distance of 50 nt).", 
+            "annotation": "Enter in box the maximal distance for merging small RNAs located less this distance apart (suggestion: 50).", 
             "id": 19, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -635,8 +640,8 @@
                 }
             ], 
             "position": {
-                "left": 1602.7999877929688, 
-                "top": 781.0500030517578
+                "left": 1602.800048828125, 
+                "top": 797.5166778564453
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -647,7 +652,7 @@
             "user_outputs": []
         }, 
         "20": {
-            "annotation": "Associate close candidates \n(use a maximal distance of 50 nt).", 
+            "annotation": "Enter in box the maximal distance for merging antisense RNAs located less this distance apart (suggestion: 50).", 
             "id": 20, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -655,7 +660,12 @@
                     "output_name": "outputFileGff"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Clusterize", 
+                    "name": "distance"
+                }
+            ], 
             "name": "Clusterize", 
             "outputs": [
                 {
@@ -668,19 +678,19 @@
                 }
             ], 
             "position": {
-                "left": 1658.0999145507812, 
-                "top": 644.2833404541016
+                "left": 1658.1000366210938, 
+                "top": 660.7500152587891
             }, 
             "post_job_actions": {}, 
             "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\": \"\\\"50\\\"\", \"colinear\": \"\\\"True\\\"\"}", 
+            "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": []
         }, 
         "21": {
-            "annotation": "Technical step: focus on 5'UTR.", 
+            "annotation": "Technical step: extracts 5'UTR features for following steps.", 
             "id": 21, 
             "input_connections": {
                 "input1": {
@@ -698,7 +708,7 @@
             ], 
             "position": {
                 "left": 1917.5667114257812, 
-                "top": 531.5166778564453
+                "top": 547.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -709,7 +719,7 @@
             "user_outputs": []
         }, 
         "22": {
-            "annotation": "Technical step: suppress \"exon\" features created by the use of the distance option in the previous clustering step.", 
+            "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": {
@@ -727,7 +737,7 @@
             ], 
             "position": {
                 "left": 1804.5667114257812, 
-                "top": 797.0500030517578
+                "top": 813.5166778564453
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -738,7 +748,7 @@
             "user_outputs": []
         }, 
         "23": {
-            "annotation": "Technical step: suppress \"exon\" features created by the use of the distance option in the previous clustering step.", 
+            "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": {
@@ -755,8 +765,8 @@
                 }
             ], 
             "position": {
-                "left": 1859.6666870117188, 
-                "top": 665.5999908447266
+                "left": 1859.6667022705078, 
+                "top": 682.0666656494141
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -767,7 +777,7 @@
             "user_outputs": []
         }, 
         "24": {
-            "annotation": "Size filter: keep 5'URT larger than the size you want (ex. specify 50 for candidates with a size of 50 or more nt).", 
+            "annotation": "Enter minimal size for calling a long 5'UTR (suggestion: 50).", 
             "id": 24, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -789,8 +799,8 @@
                 }
             ], 
             "position": {
-                "left": 2127.3333129882812, 
-                "top": 548.5166778564453
+                "left": 2132.3333740234375, 
+                "top": 570.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -801,7 +811,7 @@
             "user_outputs": []
         }, 
         "25": {
-            "annotation": "Size filter: keep small ncRNA larger than the size you want (ex. specify 50 for candidates with a size of 50 or more nt).", 
+            "annotation": "Enter minimal size for calling a small RNA (suggestion: 50).", 
             "id": 25, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -823,8 +833,8 @@
                 }
             ], 
             "position": {
-                "left": 2017.3333129882812, 
-                "top": 808.0500030517578
+                "left": 2017.3333740234375, 
+                "top": 824.5166778564453
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -835,7 +845,7 @@
             "user_outputs": []
         }, 
         "26": {
-            "annotation": "Size filter: keep antisense expression clusters larger than the size you want (ex. specify 50 for candidates with a size of 50 or more nt).", 
+            "annotation": "Enter minimal size for calling an antisense RNA (suggestion: 50).", 
             "id": 26, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -857,8 +867,8 @@
                 }
             ], 
             "position": {
-                "left": 2085.6333618164062, 
-                "top": 675.2833404541016
+                "left": 2085.6333770751953, 
+                "top": 691.7500152587891
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -869,7 +879,7 @@
             "user_outputs": []
         }, 
         "27": {
-            "annotation": "Number of overlapping reads filter: keep only 5'UTR with the number of overlapping reads  or more you want (ex. specify 10 in the input box).", 
+            "annotation": "Enter in box the minimum number of reads for calling a long 5' UTR (suggested: 10).", 
             "id": 27, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -891,8 +901,8 @@
                 }
             ], 
             "position": {
-                "left": 2344.3999633789062, 
-                "top": 561.5166778564453
+                "left": 2344.4000244140625, 
+                "top": 577.9833526611328
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -903,7 +913,7 @@
             "user_outputs": []
         }, 
         "28": {
-            "annotation": "List of small ncRNA.\nA RGB color tag is added for visualization in the Artemis environment.", 
+            "annotation": "Uses an RGB color tag for visualization of small RNAs in the Artemis environment.", 
             "id": 28, 
             "input_connections": {
                 "referenciesFile": {
@@ -920,8 +930,8 @@
                 }
             ], 
             "position": {
-                "left": 2240.9500122070312, 
-                "top": 815.6333160400391
+                "left": 2240.9500427246094, 
+                "top": 832.0999908447266
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@@ -932,7 +942,7 @@
             "user_outputs": []
         }, 
         "29": {
-            "annotation": "List of antisense expression.\nA RGB color tag is added for visualization in the Artemis environment.", 
+            "annotation": "Uses an RGB color tag for visualization of antisense RNAs in the Artemis environment.", 
             "id": 29, 
             "input_connections": {
                 "referenciesFile": {
@@ -949,8 +959,8 @@
                 }
             ], 
             "position": {
-                "left": 2305.9500122070312, 
-                "top": 686.6333160400391
+                "left": 2305.9500427246094, 
+                "top": 703.0999908447266
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@@ -961,7 +971,7 @@
             "user_outputs": []
         }, 
         "30": {
-            "annotation": "List of long 5'UTR.\nA RGB color tag is added for visualization in the Artemis environment.", 
+            "annotation": "Uses an RGB color tag for visualization of long 5' UTRs in the Artemis environment.", 
             "id": 30, 
             "input_connections": {
                 "referenciesFile": {
@@ -978,8 +988,8 @@
                 }
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             "position": {
-                "left": 2525.9500122070312, 
-                "top": 594.2666778564453
+                "left": 2525.9500732421875, 
+                "top": 610.7333526611328
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