changeset 1:267a94f068d7 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
author earlhaminst
date Mon, 20 Feb 2017 12:57:16 -0500
parents b92f5ab6d127
children 58c9294400ed
files GeneSeqToFamily.ga GeneSeqToFamily.png finding_orphan_genes.ga finding_orphan_genes.png
diffstat 4 files changed, 216 insertions(+), 179 deletions(-) [+]
line wrap: on
line diff
--- a/GeneSeqToFamily.ga	Mon Jan 09 15:06:04 2017 -0500
+++ b/GeneSeqToFamily.ga	Mon Feb 20 12:57:16 2017 -0500
@@ -12,19 +12,19 @@
             "inputs": [
                 {
                     "description": "", 
-                    "name": "CDS sequences"
+                    "name": "CDS"
                 }
             ], 
-            "label": null, 
+            "label": "CDS", 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 620, 
-                "top": 388.875
+                "left": 350.0625, 
+                "top": 418.0625
             }, 
             "tool_errors": null, 
             "tool_id": null, 
-            "tool_state": "{\"name\": \"CDS sequences\"}", 
+            "tool_state": "{\"name\": \"CDS\"}", 
             "tool_version": null, 
             "type": "data_input", 
             "uuid": "d2777a78-6429-47f6-9567-cb15140ace8d", 
@@ -44,19 +44,19 @@
             "inputs": [
                 {
                     "description": "", 
-                    "name": "Genes"
+                    "name": "Gene feature information"
                 }
             ], 
-            "label": null, 
+            "label": "Gene feature information", 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 612.8125, 
-                "top": 1110.9375
+                "left": 342.875, 
+                "top": 1140.125
             }, 
             "tool_errors": null, 
             "tool_id": null, 
-            "tool_state": "{\"name\": \"Genes\"}", 
+            "tool_state": "{\"name\": \"Gene feature information\"}", 
             "tool_version": null, 
             "type": "data_input", 
             "uuid": "3fbf4a09-9207-4a18-a133-0d865f9614f6", 
@@ -76,19 +76,19 @@
             "inputs": [
                 {
                     "description": "", 
-                    "name": "species tree"
+                    "name": "Species tree"
                 }
             ], 
-            "label": null, 
+            "label": "Species tree", 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 605.9375, 
-                "top": 1409
+                "left": 336, 
+                "top": 1438.171875
             }, 
             "tool_errors": null, 
             "tool_id": null, 
-            "tool_state": "{\"name\": \"species tree\"}", 
+            "tool_state": "{\"name\": \"Species tree\"}", 
             "tool_version": null, 
             "type": "data_input", 
             "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3", 
@@ -125,8 +125,8 @@
                 }
             ], 
             "position": {
-                "left": 847.0625, 
-                "top": 388.875
+                "left": 577.125, 
+                "top": 418.0625
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -178,8 +178,8 @@
                 }
             ], 
             "position": {
-                "left": 1094.1875, 
-                "top": 170.8125
+                "left": 824.25, 
+                "top": 199.984375
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutfile": {
@@ -235,8 +235,8 @@
                 }
             ], 
             "position": {
-                "left": 1351.4375, 
-                "top": 398.9375
+                "left": 1081.5, 
+                "top": 428.125
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput1": {
@@ -284,16 +284,10 @@
                 }
             ], 
             "position": {
-                "left": 1671.4375, 
-                "top": 472.8125
+                "left": 1401.5, 
+                "top": 502
             }, 
-            "post_job_actions": {
-                "HideDatasetActionoutput": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "output"
-                }
-            }, 
+            "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.1", 
             "tool_shed_repository": {
@@ -306,7 +300,13 @@
             "tool_version": "0.1.1", 
             "type": "tool", 
             "uuid": "3eb98d54-a52d-4605-b068-28a700290d92", 
-            "workflow_outputs": []
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "6473f6a6-9036-43f2-ba10-961cecfb351f"
+                }
+            ]
         }, 
         "7": {
             "annotation": "", 
@@ -337,8 +337,8 @@
                 }
             ], 
             "position": {
-                "left": 1907.9375, 
-                "top": 402.875
+                "left": 1638, 
+                "top": 432.0625
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutputFile": {
@@ -363,59 +363,16 @@
         }, 
         "8": {
             "annotation": "", 
-            "content_id": "Filter1", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", 
             "id": 8, 
             "input_connections": {
-                "input": {
+                "inputFile": {
                     "id": 7, 
                     "output_name": "outputFile"
                 }
             }, 
             "inputs": [
                 {
-                    "description": "runtime parameter for tool Filter", 
-                    "name": "input"
-                }
-            ], 
-            "label": null, 
-            "name": "Filter", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 2142, 
-                "top": 199
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionout_file1": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Filter1", 
-            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c2>2\\\"\", \"__page__\": 0}", 
-            "tool_version": "1.1.0", 
-            "type": "tool", 
-            "uuid": "b2126c05-5d8d-4529-84fd-1b6f7f03a0ab", 
-            "workflow_outputs": []
-        }, 
-        "9": {
-            "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.1.1", 
-            "id": 9, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 8, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [
-                {
                     "description": "runtime parameter for tool hcluster_sg_parser", 
                     "name": "inputFile"
                 }
@@ -426,11 +383,15 @@
                 {
                     "name": "ids_lists", 
                     "type": "input"
+                }, 
+                {
+                    "name": "discarded", 
+                    "type": "txt"
                 }
             ], 
             "position": {
-                "left": 2252.625, 
-                "top": 441.8125
+                "left": 1950.0625, 
+                "top": 477.171875
             }, 
             "post_job_actions": {
                 "HideDatasetActionids_lists": {
@@ -440,26 +401,32 @@
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.1.1", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", 
             "tool_shed_repository": {
-                "changeset_revision": "dbc49bd1a3e9", 
+                "changeset_revision": "17aa68582a05", 
                 "name": "hcluster_sg_parser", 
                 "owner": "earlhaminst", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "0.1.1", 
+            "tool_state": "{\"__page__\": 0, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
+            "tool_version": "0.2.0", 
             "type": "tool", 
-            "uuid": "3ad63783-ce49-4e1d-b502-3c594b0d4bd7", 
-            "workflow_outputs": []
+            "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "discarded", 
+                    "uuid": "465afc7e-afad-4228-bb28-2f7b1304a771"
+                }
+            ]
         }, 
-        "10": {
+        "9": {
             "annotation": "", 
             "content_id": "trimmer", 
-            "id": 10, 
+            "id": 9, 
             "input_connections": {
                 "input1": {
-                    "id": 9, 
+                    "id": 8, 
                     "output_name": "ids_lists"
                 }
             }, 
@@ -478,8 +445,8 @@
                 }
             ], 
             "position": {
-                "left": 1032.6875, 
-                "top": 1044
+                "left": 826.75, 
+                "top": 1053.171875
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -496,17 +463,17 @@
             "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3", 
             "workflow_outputs": []
         }, 
-        "11": {
+        "10": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8", 
-            "id": 11, 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", 
+            "id": 10, 
             "input_connections": {
                 "input_type|fasta_input": {
                     "id": 3, 
                     "output_name": "out_file1"
                 }, 
                 "input_type|identifiers": {
-                    "id": 9, 
+                    "id": 8, 
                     "output_name": "ids_lists"
                 }
             }, 
@@ -524,10 +491,6 @@
             "name": "T-Coffee", 
             "outputs": [
                 {
-                    "name": "cigar", 
-                    "type": "tabular"
-                }, 
-                {
                     "name": "clustalw_aln", 
                     "type": "clustalw"
                 }, 
@@ -569,15 +532,10 @@
                 }
             ], 
             "position": {
-                "left": 1910.9375, 
-                "top": 673.4375
+                "left": 1641, 
+                "top": 702.625
             }, 
             "post_job_actions": {
-                "HideDatasetActioncigar": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "cigar"
-                }, 
                 "HideDatasetActionclustalw_aln": {
                     "action_arguments": {}, 
                     "action_type": "HideDatasetAction", 
@@ -630,26 +588,26 @@
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", 
             "tool_shed_repository": {
-                "changeset_revision": "b3833e5b50d4", 
+                "changeset_revision": "78dd29aa7fc1", 
                 "name": "t_coffee", 
                 "owner": "earlhaminst", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
-            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"identifiers\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"fasta_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"cigar\\\", \\\"fasta_aln\\\"]\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", 
-            "tool_version": "11.0.8", 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"identifiers\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"fasta_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"fasta_aln\\\"]\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", 
+            "tool_version": "11.0.8_1", 
             "type": "tool", 
             "uuid": "827ba178-5028-4ae4-b5e1-f234bcfce9f8", 
             "workflow_outputs": []
         }, 
-        "12": {
+        "11": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", 
-            "id": 12, 
+            "id": 11, 
             "input_connections": {
                 "identifiers": {
-                    "id": 10, 
+                    "id": 9, 
                     "output_name": "out_file1"
                 }, 
                 "input": {
@@ -676,8 +634,8 @@
                 }
             ], 
             "position": {
-                "left": 1336.8125, 
-                "top": 1028.875
+                "left": 1154.875, 
+                "top": 980.0625
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -700,17 +658,17 @@
             "uuid": "b22832ea-47b0-46a1-87da-e362672133b1", 
             "workflow_outputs": []
         }, 
-        "13": {
+        "12": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", 
-            "id": 13, 
+            "id": 12, 
             "input_connections": {
                 "input1": {
-                    "id": 12, 
+                    "id": 11, 
                     "output_name": "output"
                 }, 
                 "input2": {
-                    "id": 11, 
+                    "id": 10, 
                     "output_name": "fasta_aln"
                 }
             }, 
@@ -733,8 +691,8 @@
                 }
             ], 
             "position": {
-                "left": 1643.875, 
-                "top": 1215.875
+                "left": 1373.9375, 
+                "top": 1245.0625
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -757,13 +715,13 @@
             "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", 
             "workflow_outputs": []
         }, 
-        "14": {
+        "13": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", 
-            "id": 14, 
+            "id": 13, 
             "input_connections": {
                 "aln": {
-                    "id": 13, 
+                    "id": 12, 
                     "output_name": "out_file1"
                 }, 
                 "species_tree": {
@@ -794,8 +752,8 @@
                 }
             ], 
             "position": {
-                "left": 1900.9375, 
-                "top": 1414.375
+                "left": 1631, 
+                "top": 1443.5625
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -818,21 +776,21 @@
             "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", 
             "workflow_outputs": []
         }, 
-        "15": {
+        "14": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.1.0", 
-            "id": 15, 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.2.0", 
+            "id": 14, 
             "input_connections": {
                 "alignmentFile": {
-                    "id": 11, 
-                    "output_name": "cigar"
+                    "id": 10, 
+                    "output_name": "fasta_aln"
                 }, 
                 "genesFile": {
                     "id": 1, 
                     "output_name": "output"
                 }, 
                 "treeFile": {
-                    "id": 14, 
+                    "id": 13, 
                     "output_name": "output"
                 }
             }, 
@@ -859,20 +817,20 @@
                 }
             ], 
             "position": {
-                "left": 2507.9375, 
-                "top": 1050.375
+                "left": 2238, 
+                "top": 1079.5625
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.1.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.2.0", 
             "tool_shed_repository": {
-                "changeset_revision": "af9f72ddf7f9", 
+                "changeset_revision": "fc8ca4ade638", 
                 "name": "gafa", 
                 "owner": "earlhaminst", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "tool_state": "{\"__page__\": 0, \"treeFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"alignmentFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"genesFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "0.1.0", 
+            "tool_version": "0.2.0", 
             "type": "tool", 
             "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", 
             "workflow_outputs": [
@@ -884,5 +842,5 @@
             ]
         }
     }, 
-    "uuid": "7ae94ea4-e34a-4e09-a15c-31839c6e5eef"
+    "uuid": "8a774cd5-046c-4272-badd-8e84aaed9c0f"
 }
Binary file GeneSeqToFamily.png has changed
--- a/finding_orphan_genes.ga	Mon Jan 09 15:06:04 2017 -0500
+++ b/finding_orphan_genes.ga	Mon Feb 20 12:57:16 2017 -0500
@@ -15,12 +15,12 @@
                     "name": "blast_parser data"
                 }
             ], 
-            "label": null, 
+            "label": "blast_parser data", 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 199.94483947753906, 
-                "top": 276.4521942138672
+                "left": 199.9375, 
+                "top": 276.4375
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -47,12 +47,12 @@
                     "name": "CDS"
                 }
             ], 
-            "label": null, 
+            "label": "CDS", 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 195.93748474121094, 
-                "top": 553.3639373779297
+                "left": 195.921875, 
+                "top": 553.359375
             }, 
             "tool_errors": null, 
             "tool_id": null, 
@@ -69,9 +69,41 @@
             ]
         }, 
         "2": {
+            "annotation": "List of IDs discarded from hcluster_sg results", 
+            "content_id": null, 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "List of IDs discarded from hcluster_sg results", 
+                    "name": "hcluster_sg discarded"
+                }
+            ], 
+            "label": "hcluster_sg discarded", 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 191, 
+                "top": 697
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"hcluster_sg discarded\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "3866a37f-3309-4c5d-8ed9-bb7c21d25d8a", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "f9fe709d-8a1b-44b0-9989-688af44b16ad"
+                }
+            ]
+        }, 
+        "3": {
             "annotation": "", 
             "content_id": "Cut1", 
-            "id": 2, 
+            "id": 3, 
             "input_connections": {
                 "input": {
                     "id": 0, 
@@ -93,8 +125,8 @@
                 }
             ], 
             "position": {
-                "left": 429.9632110595703, 
-                "top": 276.4521942138672
+                "left": 429.953125, 
+                "top": 276.4375
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -111,10 +143,10 @@
             "uuid": "3d809485-291c-4858-ade6-2f465bf667f0", 
             "workflow_outputs": []
         }, 
-        "3": {
+        "4": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0", 
-            "id": 3, 
+            "id": 4, 
             "input_connections": {
                 "input": {
                     "id": 1, 
@@ -136,8 +168,8 @@
                 }
             ], 
             "position": {
-                "left": 429.9632110595703, 
-                "top": 389.44850158691406
+                "left": 429.953125, 
+                "top": 389.4375
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -160,13 +192,13 @@
             "uuid": "614def54-f941-49a4-950c-69f651e6b35f", 
             "workflow_outputs": []
         }, 
-        "4": {
+        "5": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", 
-            "id": 4, 
+            "id": 5, 
             "input_connections": {
                 "infile": {
-                    "id": 2, 
+                    "id": 3, 
                     "output_name": "out_file1"
                 }
             }, 
@@ -185,8 +217,8 @@
                 }
             ], 
             "position": {
-                "left": 659.9999542236328, 
-                "top": 199.94483947753906
+                "left": 659.984375, 
+                "top": 199.9375
             }, 
             "post_job_actions": {
                 "HideDatasetActionoutfile": {
@@ -209,13 +241,13 @@
             "uuid": "55da94d2-b1d9-46ed-9668-db9b7f19a5bb", 
             "workflow_outputs": []
         }, 
-        "5": {
+        "6": {
             "annotation": "", 
             "content_id": "Cut1", 
-            "id": 5, 
+            "id": 6, 
             "input_connections": {
                 "input": {
-                    "id": 3, 
+                    "id": 4, 
                     "output_name": "output"
                 }
             }, 
@@ -234,8 +266,8 @@
                 }
             ], 
             "position": {
-                "left": 675.9558258056641, 
-                "top": 389.44850158691406
+                "left": 675.953125, 
+                "top": 389.4375
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -252,13 +284,13 @@
             "uuid": "5bae54ed-b8c8-432c-9980-422d0f678be3", 
             "workflow_outputs": []
         }, 
-        "6": {
+        "7": {
             "annotation": "", 
             "content_id": "Cut1", 
-            "id": 6, 
+            "id": 7, 
             "input_connections": {
                 "input": {
-                    "id": 4, 
+                    "id": 5, 
                     "output_name": "outfile"
                 }
             }, 
@@ -277,8 +309,8 @@
                 }
             ], 
             "position": {
-                "left": 917.9411773681641, 
-                "top": 198.47425842285156
+                "left": 917.9375, 
+                "top": 198.46875
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -295,17 +327,17 @@
             "uuid": "d6dc6ba2-efc0-4e90-8562-4739c4f41fab", 
             "workflow_outputs": []
         }, 
-        "7": {
+        "8": {
             "annotation": "", 
             "content_id": "comp1", 
-            "id": 7, 
+            "id": 8, 
             "input_connections": {
                 "input1": {
-                    "id": 5, 
+                    "id": 6, 
                     "output_name": "out_file1"
                 }, 
                 "input2": {
-                    "id": 6, 
+                    "id": 7, 
                     "output_name": "out_file1"
                 }
             }, 
@@ -328,8 +360,8 @@
                 }
             ], 
             "position": {
-                "left": 1123.952163696289, 
-                "top": 363.4558563232422
+                "left": 1123.9375, 
+                "top": 363.453125
             }, 
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -346,13 +378,60 @@
             "uuid": "7c71fbae-828d-4c99-8f7b-fe1a90b27626", 
             "workflow_outputs": []
         }, 
-        "8": {
+        "9": {
+            "annotation": "", 
+            "content_id": "cat1", 
+            "id": 9, 
+            "input_connections": {
+                "input1": {
+                    "id": 8, 
+                    "output_name": "out_file1"
+                }, 
+                "queries_0|input2": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Concatenate datasets", 
+                    "name": "input1"
+                }
+            ], 
+            "label": null, 
+            "name": "Concatenate datasets", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1130.5, 
+                "top": 686
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "cat1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"queries\": \"[{\\\"input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__index__\\\": 0}]\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "uuid": "8a1e29ca-8dec-4143-9db1-f38f820b0e9a", 
+            "workflow_outputs": []
+        }, 
+        "10": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", 
-            "id": 8, 
+            "id": 10, 
             "input_connections": {
                 "identifiers": {
-                    "id": 7, 
+                    "id": 9, 
                     "output_name": "out_file1"
                 }, 
                 "input": {
@@ -379,8 +458,8 @@
                 }
             ], 
             "position": {
-                "left": 1129.9264068603516, 
-                "top": 544.4669036865234
+                "left": 1392.921875, 
+                "top": 550.453125
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -404,5 +483,5 @@
             ]
         }
     }, 
-    "uuid": "23e0aa20-d91a-429e-817c-654a67b0a171"
-}
\ No newline at end of file
+    "uuid": "cf6b9210-2ed8-46b1-920e-ac6303ed44d5"
+}
Binary file finding_orphan_genes.png has changed