comparison rxlr_venn_workflow.ga @ 12:923fa2577564 draft

Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.

11:de29af5da85e

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "3 RXLR methods, Venn Diagram, overlap FASTA", 
    "steps": {
        "0": {
            "annotation": "", 

                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}", 
            "tool_version": "0.0.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 

                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}", 
            "tool_version": "0.0.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 

                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}", 
            "tool_version": "0.0.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 

                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {

                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {

                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {

                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {

                    "output_name": "PDF"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "venn_list", 
            "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\"}", 
            "tool_version": "0.0.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {

                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {

                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }
    }

12:923fa2577564

{
    "a_galaxy_workflow": "true", 
    "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2013).", 
    "format-version": "0.1", 
    "name": "3 RXLR methods, Venn Diagram, overlap FASTA", 
    "steps": {
        "0": {
            "annotation": "", 

                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}", 
            "tool_version": "0.0.7", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "", 

                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}", 
            "tool_version": "0.0.7", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "", 

                    "output_name": "tabular_file"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "rxlr_motifs", 
            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}", 
            "tool_version": "0.0.7", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "", 

                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {

                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {

                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "Filter1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {

                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {

                    "output_name": "PDF"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "venn_list", 
            "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "0.0.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {

                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {

                    "output_name": "output_pos"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "seq_filter_by_id", 
            "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 
            "tool_version": "0.0.5", 
            "type": "tool", 
            "user_outputs": []
        }
    }