Mercurial > repos > clairetn > detrprok_wf

changeset 8:ce067ea5f1e0 draft

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Uploaded
author clairetn
date Thu, 21 Mar 2013 15:26:28 -0400
parents 158f0fdfd552
children f0ca0981eb86
files Galaxy-Workflow-_DetR_Prok_v3__.ga
diffstat 1 files changed, 41 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/Galaxy-Workflow-_DetR_Prok_v3__.ga	Wed Mar 20 10:06:30 2013 -0400
+++ b/Galaxy-Workflow-_DetR_Prok_v3__.ga	Thu Mar 21 15:26:28 2013 -0400
@@ -41,7 +41,7 @@
             "outputs": [], 
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@@ -98,7 +98,7 @@
             ], 
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@@ -147,7 +147,7 @@
             "user_outputs": []
         }, 
         "5": {
-            "annotation": "Clusters overlaping reads of same direction to produce read clusters.", 
+            "annotation": "In box, enter the maximal distance used to cluster reads of same direction for read clusters definition. This distance depends on the deepness of the RNAseq (ex. a value of 0 will cluster only overlapping reads and a value of 20 will cluster reads even if they are 20-nt apart).", 
             "id": 5, 
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@@ -174,7 +174,7 @@
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@@ -212,7 +212,7 @@
             ], 
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@@ -223,7 +223,7 @@
             "user_outputs": []
         }, 
         "7": {
-            "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!", 
+            "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! (15 was suggested)", 
             "id": 7, 
             "input_connections": {
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@@ -250,7 +250,7 @@
             ], 
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@@ -294,7 +294,7 @@
             "user_outputs": []
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         "9": {
-            "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.", 
+            "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 extended CDS.", 
             "id": 9, 
             "input_connections": {
                 "formatType|inputFileName": {
@@ -320,7 +320,7 @@
                 }
             ], 
             "position": {
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@@ -379,7 +379,7 @@
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@@ -390,7 +390,7 @@
             "user_outputs": []
         }, 
         "12": {
-            "annotation": "Splits transcription units into UTRs, CDS and/or operon spacers.", 
+            "annotation": "Splits extended CDS into UTRs, CDS and/or operon spacers.", 
             "id": 12, 
             "input_connections": {
                 "referenciesFile": {
@@ -412,7 +412,7 @@
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@@ -423,7 +423,7 @@
             "user_outputs": []
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         "13": {
-            "annotation": "Selection of read clusters that are outside and not in antisense of transcription units. This step produces the first list of small RNAs.", 
+            "annotation": "Selection of read clusters that are outside and not in antisense of extended CDS. This step produces the first list of small RNAs.", 
             "id": 13, 
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@@ -445,18 +445,18 @@
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-            "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}\"}", 
+            "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", 
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         "14": {
-            "annotation": "Selection of read clusters that are antisense of the transcription units.", 
+            "annotation": "Selection of read clusters that are antisense of the extended CDS. This step produces the first list of antisense candidates.", 
             "id": 14, 
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@@ -478,12 +478,12 @@
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+            "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}\"}", 
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@@ -510,8 +510,8 @@
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@@ -545,7 +545,7 @@
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@@ -579,7 +579,7 @@
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@@ -607,8 +607,8 @@
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@@ -640,8 +640,8 @@
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@@ -679,7 +679,7 @@
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@@ -765,8 +765,8 @@
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