# HG changeset patch # User clairetn # Date 1363893988 14400 # Node ID ce067ea5f1e004f3c4714f17deb3925f9db0df81 # Parent 158f0fdfd5522ebb12ac1bf9b546a03ddd1b0764 Uploaded diff -r 158f0fdfd552 -r ce067ea5f1e0 Galaxy-Workflow-_DetR_Prok_v3__.ga --- 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": [], "position": { "left": 215.9000244140625, - "top": 484.9833526611328 + "top": 484.98333740234375 }, "tool_errors": null, "tool_id": null, @@ -98,7 +98,7 @@ ], "position": { "left": 418.666748046875, - "top": 479.9833526611328 + "top": 479.98333740234375 }, "post_job_actions": {}, "tool_errors": null, @@ -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, "input_connections": { "formatType|inputFileName": { @@ -174,7 +174,7 @@ ], "position": { "left": 496.433349609375, - "top": 596.9833526611328 + "top": 596.9833374023438 }, "post_job_actions": {}, "tool_errors": null, @@ -212,7 +212,7 @@ ], "position": { "left": 655.2000732421875, - "top": 433.9833526611328 + "top": 433.98333740234375 }, "post_job_actions": {}, "tool_errors": null, @@ -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": { "formatType2|inputFileName2": { @@ -250,7 +250,7 @@ ], "position": { "left": 742.2000732421875, - "top": 588.7500152587891 + "top": 588.75 }, "post_job_actions": {}, "tool_errors": null, @@ -294,7 +294,7 @@ "user_outputs": [] }, "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": { - "left": 1036.7333984375, + "left": 1036.7333679199219, "top": 307.98333740234375 }, "post_job_actions": {}, @@ -379,7 +379,7 @@ ], "position": { "left": 973.2667236328125, - "top": 460.9833526611328 + "top": 460.98333740234375 }, "post_job_actions": {}, "tool_errors": null, @@ -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 @@ ], "position": { "left": 1215.2833862304688, - "top": 452.0166778564453 + "top": 452.01666259765625 }, "post_job_actions": {}, "tool_errors": null, @@ -423,7 +423,7 @@ "user_outputs": [] }, "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, "input_connections": { "formatType2|inputFileName2": { @@ -445,18 +445,18 @@ ], "position": { "left": 1068.0333862304688, - "top": 766.5166778564453 + "top": 766.5166320800781 }, "post_job_actions": {}, "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}\"}", + "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": [] }, "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, "input_connections": { "formatType2|inputFileName2": { @@ -478,12 +478,12 @@ ], "position": { "left": 1170.0333862304688, - "top": 618.7500152587891 + "top": 618.75 }, "post_job_actions": {}, "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\": \"{\\\"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\": \"\\\"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_version": "1.0.0", "type": "tool", "user_outputs": [] @@ -510,8 +510,8 @@ } ], "position": { - 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