annotate Galaxy-Workflow-TR_genome_profiling.ga @ 0:70f8259b0b30 draft

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author arkarachai-fungtammasan
date Wed, 01 Apr 2015 16:48:58 -0400
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184 "tool_id": "Cut1",
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185 "tool_state": "{\"columnList\": \"\\\"c6,c2,c9,c4,c1,c10\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
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186 "tool_version": "1.0.2",
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187 "type": "tool",
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188 "user_outputs": []
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189 }
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190 }
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191 }