diff Galaxy-Workflow-SNiPlay_Workflow.ga @ 1:6c3581822cad draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-SNiPlay_Workflow.ga	Wed Oct 14 05:31:37 2015 -0400
@@ -0,0 +1,728 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "SNiPlay Workflow", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "156cb9d1-fff4-4c22-8eb8-6c7e8b6f891c"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 320
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "4005036f-e5fd-4f8b-8eac-68d0872a77e4"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 440
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "6088050b-e81a-4f1a-8e38-192974d0c711"
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "genome": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "gff": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "vcf": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "SnpEff", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "statsFile", 
+                    "type": "html"
+                }, 
+                {
+                    "name": "log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 424, 
+                "top": 111
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/4.0", 
+            "tool_state": "{\"__page__\": 0, \"vcf\": \"null\", \"gff\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"genome\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "4.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "84ba0275-3db8-4106-b725-9626f5f78c2e"
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "SnpSift Filter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }
+            ], 
+            "position": {
+                "left": 640, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.0.0", 
+            "tool_state": "{\"__page__\": 0, \"filtering\": \"{\\\"mode\\\": \\\"entries\\\", \\\"__current_case__\\\": 0}\", \"expr\": \"\\\"( QUAL > 3 )\\\"\", \"__rerun_remap_job_id__\": null, \"inverse\": \"\\\"False\\\"\", \"input\": \"null\"}", 
+            "tool_version": "4.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "5139c1e1-6155-4881-9257-136c8ea9213a"
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "filein": {
+                    "id": 4, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "VCFtools Filter", 
+            "outputs": [
+                {
+                    "name": "fileout", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "fileout_map", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "filelog", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 860, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"None\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"export\": \"\\\"VCF\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"filein\": \"null\", \"samples\": \"\\\"None\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "f4296cba-1369-4e44-97c9-2e1c1f4955cb"
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "filein": {
+                    "id": 5, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "VCFtools Filter", 
+            "outputs": [
+                {
+                    "name": "fileout", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "fileout_map", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "filelog", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1080, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"export\": \"\\\"plink\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"filein\": \"null\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "8e4bd231-e134-42dc-9457-5c0738b8c46a"
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "filein": {
+                    "id": 5, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "VCFtools Stats", 
+            "outputs": [
+                {
+                    "name": "fileout_annot", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout_het", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout_imiss", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout_sum", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "filelog", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1080, 
+                "top": 320
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsstats/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"vcf_stats\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "32da698d-fcab-4da7-a0c2-deace884d47e"
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "filein": {
+                    "id": 5, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "VCF tools SlidingWindow", 
+            "outputs": [
+                {
+                    "name": "fileout_snp", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "fileout_taj", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "fileout_tstv", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "fileout_windowed", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "filelog", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1080, 
+                "top": 440
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsslidingwindow/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"step\": \"\\\"50000\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"snp_density\\\"\", \"window\": \"\\\"200000\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "25ee9e9a-00f0-484b-bf48-685193d95882"
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "filein": {
+                    "id": 5, 
+                    "output_name": "fileout"
+                }, 
+                "optional|filefasta": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "optional|filegff": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "VCF to Hapmap", 
+            "outputs": [
+                {
+                    "name": "fileout", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout_seq", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout_fa1", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 1080, 
+                "top": 560
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_vcf2fastaandhapmap/1.1.0", 
+            "tool_state": "{\"__page__\": 0, \"optional\": \"{\\\"file_opt\\\": \\\"fasta_gff\\\", \\\"filefasta\\\": null, \\\"filegff\\\": null, \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"input\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "123f77f8-3fd2-4579-9d0f-74b0aab7a5ae"
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "map": {
+                    "id": 6, 
+                    "output_name": "fileout_map"
+                }, 
+                "ped": {
+                    "id": 6, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "plink: ped2bed", 
+            "outputs": [
+                {
+                    "name": "bed", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fam", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "bim", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "logs", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1300, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/ped2bed/1.24", 
+            "tool_state": "{\"map\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"ped\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.24", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "30c86fbf-9815-4d5a-b5ee-ae8ea9a67cec"
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "filein": {
+                    "id": 6, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Ped2Fasta", 
+            "outputs": [
+                {
+                    "name": "fileout", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 1300, 
+                "top": 320
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_pedToFasta/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "ba6bfbda-00b1-41fa-b731-b416db10f9dd"
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "filemap": {
+                    "id": 6, 
+                    "output_name": "fileout_map"
+                }, 
+                "fileped": {
+                    "id": 6, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "MDS plot", 
+            "outputs": [
+                {
+                    "name": "fileout_matrix", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "fileout_plot", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "fileout_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1300, 
+                "top": 680
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_mdsplot/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"fileped\": \"null\", \"filemap\": \"null\", \"__rerun_remap_job_id__\": null, \"fileout_label\": \"\\\"mdsplot\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "c912f3bf-23e5-4bb0-9a0f-516828c9d4db"
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "filein": {
+                    "id": 9, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "SNP density", 
+            "outputs": [
+                {
+                    "name": "fileout", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "fileout_bysample", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1300, 
+                "top": 440
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_density/1.2.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"densities\\\"\", \"step\": \"\\\"200000\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.2.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "a7524249-d521-42b8-bf9e-953a4807b46b"
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "input": {
+                    "id": 9, 
+                    "output_name": "fileout_fa1"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Diversity by gene", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1300, 
+                "top": 560
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/calculate_diversity/2.1.6", 
+            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"__page__\": 0}", 
+            "tool_version": "2.1.6", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "f1b611d0-ae04-4ee0-ba80-e7d5154b77db"
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "bed": {
+                    "id": 10, 
+                    "output_name": "bed"
+                }, 
+                "bim": {
+                    "id": 10, 
+                    "output_name": "bim"
+                }, 
+                "fam": {
+                    "id": 10, 
+                    "output_name": "fam"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Admixture", 
+            "outputs": [
+                {
+                    "name": "best_k_output", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "best_k_logfile", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "outputs", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "logs", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1520, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/admixture/admixture/1.23", 
+            "tool_state": "{\"__page__\": 0, \"bim\": \"null\", \"__rerun_remap_job_id__\": null, \"kmin\": \"\\\"1\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"kmax\": \"\\\"5\\\"\", \"bed\": \"null\", \"fam\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.23", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "3fcde6c6-747d-416b-9594-d4f5e3ed565e"
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "filein": {
+                    "id": 11, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Readseq", 
+            "outputs": [
+                {
+                    "name": "fileout_log", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1520, 
+                "top": 320
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/readseq/sniplay_readseq/1.0.2", 
+            "tool_state": "{\"__page__\": 0, \"format\": \"\\\"12\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"phylip conversion\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "b9dff56a-5a08-47e3-9f89-1cffb294230c"
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "input_data": {
+                    "id": 16, 
+                    "output_name": "fileout_log"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "FastME", 
+            "outputs": [
+                {
+                    "name": "fileout_log", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1740, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/fastme/sniplay_fastme/1.0.2", 
+            "tool_state": "{\"distance\": \"\\\"I\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"Newick tree\\\"\", \"input_data\": \"null\", \"model\": \"\\\"4\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "0fd8a01b-9dd4-4347-a68c-6c7c4c6c077b"
+        }, 
+        "18": {
+            "annotation": "", 
+            "id": 18, 
+            "input_connections": {
+                "filein": {
+                    "id": 17, 
+                    "output_name": "fileout"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Rooting", 
+            "outputs": [
+                {
+                    "name": "fileout_log", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fileout", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1960, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/1.0.2", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"out tree\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "a3bf63b2-f630-438c-8bdb-4800dbf0c84d"
+        }
+    }, 
+    "uuid": "787a27ea-111f-4e9b-b3e9-a649b0d41af8"
+}
\ No newline at end of file