amrplusplus_workflow: amrplusplus

author	chrisd
date	Sun, 27 Mar 2016 02:42:55 -0400
parents
children

rev	line source
4 d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	1 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	2 "a_galaxy_workflow": "true",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	3 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	4 "format-version": "0.1",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	5 "name": "amrplusplus_wf_pe",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	6 "steps": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	7 "0": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	8 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	9 "content_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	10 "id": 0,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	11 "input_connections": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	12 "inputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	13 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	14 "description": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	15 "name": "Input Dataset"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	16 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	17 ],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	18 "label": "AMR Database",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	19 "name": "Input dataset",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	20 "outputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	21 "position": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	22 "left": 200,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	23 "top": 200
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	24 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	25 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	26 "tool_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	27 "tool_state": "{\"name\": \"Input Dataset\"}",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	28 "tool_version": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	29 "type": "data_input",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	30 "uuid": "c33b3302-86dd-4020-920b-e91904994b0b",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	31 "workflow_outputs": []
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	32 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	33 "1": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	34 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	35 "content_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	36 "id": 1,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	37 "input_connections": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	38 "inputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	39 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	40 "description": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	41 "name": "Input Dataset"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	42 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	43 ],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	44 "label": "Host Genome",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	45 "name": "Input dataset",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	46 "outputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	47 "position": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	48 "left": 200,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	49 "top": 285
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	50 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	51 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	52 "tool_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	53 "tool_state": "{\"name\": \"Input Dataset\"}",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	54 "tool_version": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	55 "type": "data_input",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	56 "uuid": "828c1738-4db6-4548-89b8-85e68a00491a",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	57 "workflow_outputs": []
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	58 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	59 "2": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	60 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	61 "content_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	62 "id": 2,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	63 "input_connections": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	64 "inputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	65 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	66 "description": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	67 "name": "Input Dataset"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	68 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	69 ],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	70 "label": "FastQ Forward",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	71 "name": "Input dataset",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	72 "outputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	73 "position": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	74 "left": 200,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	75 "top": 370
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	76 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	77 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	78 "tool_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	79 "tool_state": "{\"name\": \"Input Dataset\"}",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	80 "tool_version": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	81 "type": "data_input",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	82 "uuid": "1956acf3-af87-497d-bced-1dc18003b4ee",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	83 "workflow_outputs": []
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	84 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	85 "3": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	86 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	87 "content_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	88 "id": 3,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	89 "input_connections": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	90 "inputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	91 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	92 "description": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	93 "name": "Input Dataset"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	94 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	95 ],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	96 "label": "FastQ Reverse",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	97 "name": "Input dataset",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	98 "outputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	99 "position": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	100 "left": 200,
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	103 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	104 "tool_id": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	105 "tool_state": "{\"name\": \"Input Dataset\"}",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	106 "tool_version": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	107 "type": "data_input",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	108 "uuid": "0e020fbd-697d-4ebc-bd3d-0b45d5104b44",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	109 "workflow_outputs": []
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	110 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	111 "4": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	112 "annotation": "",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	114 "id": 4,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	115 "input_connections": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	116 "paired_end\|paired_input_type_conditional\|fastq_r1_in": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	117 "id": 2,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	118 "output_name": "output"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	119 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	120 "paired_end\|paired_input_type_conditional\|fastq_r2_in": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	121 "id": 3,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	122 "output_name": "output"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	123 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	124 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	125 "inputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	126 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	127 "name": "Trimmomatic",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	128 "outputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	129 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	131 "type": "input"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	132 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	133 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	135 "type": "input"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	136 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	137 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	138 "name": "fastq_out_r1_paired",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	139 "type": "fastqsanger"
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	141 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	143 "type": "fastqsanger"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	144 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	145 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	147 "type": "fastqsanger"
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	149 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	151 "type": "fastqsanger"
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	157 ],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	158 "position": {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	160 "top": 200
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	162 "post_job_actions": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	163 "DeleteIntermediatesActionfastq_out_paired": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	164 "action_arguments": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	165 "action_type": "DeleteIntermediatesAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	166 "output_name": "fastq_out_paired"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	167 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	168 "HideDatasetActionfastq_out": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	169 "action_arguments": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	170 "action_type": "HideDatasetAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	171 "output_name": "fastq_out"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	172 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	173 "HideDatasetActionfastq_out_paired": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	174 "action_arguments": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	175 "action_type": "HideDatasetAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	176 "output_name": "fastq_out_paired"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	177 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	178 "HideDatasetActionfastq_out_r1_unpaired": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	179 "action_arguments": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	180 "action_type": "HideDatasetAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	181 "output_name": "fastq_out_r1_unpaired"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	182 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	183 "HideDatasetActionfastq_out_r2_unpaired": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	184 "action_arguments": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	185 "action_type": "HideDatasetAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	186 "output_name": "fastq_out_r2_unpaired"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	187 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	188 "HideDatasetActionfastq_out_unpaired": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	189 "action_arguments": {},
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	190 "action_type": "HideDatasetAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	191 "output_name": "fastq_out_unpaired"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	192 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	193 },
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	209 "uuid": "29696b1d-f675-4255-b902-f7ded1cf6fad"
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	225 },
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	247 "action_type": "DeleteIntermediatesAction",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	249 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	250 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	251 "tool_errors": null,
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	253 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	255 "type": "tool",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	256 "uuid": "ddf4de24-ceec-4dd7-a4a2-cd91994b4346",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	257 "workflow_outputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	258 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	260 "output_name": "bam_output",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	261 "uuid": "ad467c2c-4b48-4f06-9c68-ced14296afb8"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	262 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	263 ]
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	264 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	265 "6": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	266 "annotation": "",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	268 "id": 6,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	269 "input_connections": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	270 "inputFile": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	271 "id": 5,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	272 "output_name": "bam_output"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	273 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	274 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	275 "inputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	276 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	277 "name": "FilterSamReads",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	293 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	294 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	295 "tool_errors": null,
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	297 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	306 }
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	339 "action_type": "DeleteIntermediatesAction",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	341 }
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	343 "tool_errors": null,
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	345 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": null, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"__current_case__\\\": 3, \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	350 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	353 "uuid": "981cdac9-e993-471c-87c2-c667431ed47f"
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	356 },
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	364 "output_name": "bam_output"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	365 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	366 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	367 "inputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	368 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	369 "name": "SortSam",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	370 "outputs": [
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	385 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	386 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	387 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	388 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	389 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	391 "type": "tool",
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	393 "workflow_outputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	394 {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	398 }
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	400 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	401 "9": {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	404 "id": 9,
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	408 "output_name": "outFile"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	409 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	410 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	411 "inputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	412 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	413 "name": "BAM-to-SAM",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	414 "outputs": [
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	424 "post_job_actions": {
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	427 "action_type": "DeleteIntermediatesAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	428 "output_name": "output1"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	429 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	430 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	431 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	432 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	433 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	434 "tool_version": "2.0",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	435 "type": "tool",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	436 "uuid": "9fe23b03-b221-4007-a406-44b05be85066",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	437 "workflow_outputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	438 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	439 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	440 "output_name": "output1",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	441 "uuid": "c34f9ca8-8d2d-4d8a-bb24-c3a030ff45af"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	442 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	443 ]
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	444 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	445 "10": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	446 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	447 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	448 "id": 10,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	449 "input_connections": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	450 "input1": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	451 "id": 0,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	452 "output_name": "output"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	453 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	454 "input2": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	455 "id": 9,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	456 "output_name": "output1"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	457 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	458 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	459 "inputs": [],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	460 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	461 "name": "Coverage Sampler",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	462 "outputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	463 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	464 "name": "output1",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	465 "type": "tabular"
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d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	467 ],
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	468 "position": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	469 "left": 2184,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	470 "top": 200
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	471 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	472 "post_job_actions": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	473 "RenameDatasetActionoutput1": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	474 "action_arguments": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	475 "newname": "Coverage Results"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	476 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	477 "action_type": "RenameDatasetAction",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	478 "output_name": "output1"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	479 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	480 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	481 "tool_errors": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	482 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	483 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	484 "tool_version": "0.1.0",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	485 "type": "tool",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	486 "uuid": "8305b84c-ceb2-41bb-9f07-4c7bedff5d0a",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	487 "workflow_outputs": [
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	488 {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	489 "label": null,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	490 "output_name": "output1",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	491 "uuid": "1db38476-e927-44aa-bac5-0ff46b81a2b7"
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	492 }
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	493 ]
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	494 },
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	495 "11": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	496 "annotation": "",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	497 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	498 "id": 11,
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	499 "input_connections": {
d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368 chrisd parents: diff changeset	500 "input1": {

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1 {

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2 "a_galaxy_workflow": "true",

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3 "annotation": "",

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4 "format-version": "0.1",

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5 "name": "amrplusplus_wf_pe",

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6 "steps": {

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7 "0": {

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8 "annotation": "",

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9 "content_id": null,

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10 "id": 0,

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11 "input_connections": {},

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12 "inputs": [

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13 {

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14 "description": "",

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15 "name": "Input Dataset"

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16 }

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17 ],

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18 "label": "AMR Database",

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19 "name": "Input dataset",

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20 "outputs": [],

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21 "position": {

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22 "left": 200,

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23 "top": 200

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24 },

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25 "tool_errors": null,

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26 "tool_id": null,

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27 "tool_state": "{\"name\": \"Input Dataset\"}",

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28 "tool_version": null,

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29 "type": "data_input",

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30 "uuid": "c33b3302-86dd-4020-920b-e91904994b0b",

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31 "workflow_outputs": []

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32 },

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33 "1": {

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34 "annotation": "",

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35 "content_id": null,

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36 "id": 1,

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37 "input_connections": {},

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38 "inputs": [

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39 {

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40 "description": "",

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41 "name": "Input Dataset"

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42 }

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43 ],

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44 "label": "Host Genome",

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45 "name": "Input dataset",

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46 "outputs": [],

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47 "position": {

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48 "left": 200,

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49 "top": 285

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50 },

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51 "tool_errors": null,

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52 "tool_id": null,

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53 "tool_state": "{\"name\": \"Input Dataset\"}",

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54 "tool_version": null,

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55 "type": "data_input",

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56 "uuid": "828c1738-4db6-4548-89b8-85e68a00491a",

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57 "workflow_outputs": []

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58 },

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59 "2": {

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60 "annotation": "",

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61 "content_id": null,

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62 "id": 2,

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63 "input_connections": {},

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64 "inputs": [

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65 {

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66 "description": "",

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67 "name": "Input Dataset"

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68 }

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69 ],

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70 "label": "FastQ Forward",

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71 "name": "Input dataset",

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72 "outputs": [],

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73 "position": {

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74 "left": 200,

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75 "top": 370

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76 },

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77 "tool_errors": null,

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78 "tool_id": null,

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79 "tool_state": "{\"name\": \"Input Dataset\"}",

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80 "tool_version": null,

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81 "type": "data_input",

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82 "uuid": "1956acf3-af87-497d-bced-1dc18003b4ee",

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83 "workflow_outputs": []

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84 },

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85 "3": {

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86 "annotation": "",

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87 "content_id": null,

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88 "id": 3,

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89 "input_connections": {},

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90 "inputs": [

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91 {

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92 "description": "",

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93 "name": "Input Dataset"

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94 }

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95 ],

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96 "label": "FastQ Reverse",

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97 "name": "Input dataset",

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98 "outputs": [],

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99 "position": {

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100 "left": 200,

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101 "top": 455

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102 },

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103 "tool_errors": null,

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104 "tool_id": null,

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105 "tool_state": "{\"name\": \"Input Dataset\"}",

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106 "tool_version": null,

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107 "type": "data_input",

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108 "uuid": "0e020fbd-697d-4ebc-bd3d-0b45d5104b44",

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109 "workflow_outputs": []

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110 },

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111 "4": {

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112 "annotation": "",

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113 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",

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114 "id": 4,

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115 "input_connections": {

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116 "paired_end|paired_input_type_conditional|fastq_r1_in": {

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117 "id": 2,

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118 "output_name": "output"

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119 },

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120 "paired_end|paired_input_type_conditional|fastq_r2_in": {

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121 "id": 3,

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122 "output_name": "output"

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123 }

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124 },

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125 "inputs": [],

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126 "label": null,

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127 "name": "Trimmomatic",

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128 "outputs": [

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129 {

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130 "name": "fastq_out_paired",

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131 "type": "input"

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132 },

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133 {

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134 "name": "fastq_out_unpaired",

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135 "type": "input"

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136 },

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137 {

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138 "name": "fastq_out_r1_paired",

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139 "type": "fastqsanger"

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140 },

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141 {

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142 "name": "fastq_out_r2_paired",

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143 "type": "fastqsanger"

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144 },

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145 {

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146 "name": "fastq_out_r1_unpaired",

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147 "type": "fastqsanger"

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148 },

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149 {

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150 "name": "fastq_out_r2_unpaired",

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151 "type": "fastqsanger"

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152 },

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153 {

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154 "name": "fastq_out",

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155 "type": "fastqsanger"

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156 }

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157 ],

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158 "position": {

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159 "left": 435,

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160 "top": 200

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161 },

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162 "post_job_actions": {

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163 "DeleteIntermediatesActionfastq_out_paired": {

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164 "action_arguments": {},

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165 "action_type": "DeleteIntermediatesAction",

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166 "output_name": "fastq_out_paired"

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167 },

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168 "HideDatasetActionfastq_out": {

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169 "action_arguments": {},

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170 "action_type": "HideDatasetAction",

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171 "output_name": "fastq_out"

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172 },

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173 "HideDatasetActionfastq_out_paired": {

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174 "action_arguments": {},

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175 "action_type": "HideDatasetAction",

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176 "output_name": "fastq_out_paired"

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177 },

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178 "HideDatasetActionfastq_out_r1_unpaired": {

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179 "action_arguments": {},

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180 "action_type": "HideDatasetAction",

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181 "output_name": "fastq_out_r1_unpaired"

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182 },

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183 "HideDatasetActionfastq_out_r2_unpaired": {

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184 "action_arguments": {},

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185 "action_type": "HideDatasetAction",

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186 "output_name": "fastq_out_r2_unpaired"

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187 },

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188 "HideDatasetActionfastq_out_unpaired": {

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189 "action_arguments": {},

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190 "action_type": "HideDatasetAction",

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191 "output_name": "fastq_out_unpaired"

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192 }

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193 },

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194 "tool_errors": null,

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195 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",

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196 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}",

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197 "tool_version": "0.32.3",

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198 "type": "tool",

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199 "uuid": "68fbd2ce-d667-4f34-a3e0-4381d93bfbaa",

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200 "workflow_outputs": [

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201 {

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202 "label": null,

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203 "output_name": "fastq_out_r1_paired",

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204 "uuid": "59ce771e-1cad-486b-ab2e-3ed1c85a195c"

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205 },

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206 {

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207 "label": null,

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208 "output_name": "fastq_out_r2_paired",

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209 "uuid": "29696b1d-f675-4255-b902-f7ded1cf6fad"

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210 }

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211 ]

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212 },

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213 "5": {

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214 "annotation": "",

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215 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",

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216 "id": 5,

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217 "input_connections": {

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218 "input_type|fastq_input1": {

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219 "id": 4,

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220 "output_name": "fastq_out_r1_paired"

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221 },

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222 "input_type|fastq_input2": {

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223 "id": 4,

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224 "output_name": "fastq_out_r2_paired"

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225 },

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226 "reference_source|ref_file": {

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227 "id": 1,

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228 "output_name": "output"

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229 }

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230 },

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231 "inputs": [],

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232 "label": null,

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233 "name": "Map with BWA",

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234 "outputs": [

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235 {

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236 "name": "bam_output",

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237 "type": "bam"

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238 }

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239 ],

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240 "position": {

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241 "left": 763,

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242 "top": 200

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243 },

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244 "post_job_actions": {

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245 "DeleteIntermediatesActionbam_output": {

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246 "action_arguments": {},

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247 "action_type": "DeleteIntermediatesAction",

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248 "output_name": "bam_output"

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249 }

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250 },

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251 "tool_errors": null,

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252 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",

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253 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",

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254 "tool_version": "0.7.12.1",

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255 "type": "tool",

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256 "uuid": "ddf4de24-ceec-4dd7-a4a2-cd91994b4346",

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257 "workflow_outputs": [

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258 {

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259 "label": null,

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260 "output_name": "bam_output",

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261 "uuid": "ad467c2c-4b48-4f06-9c68-ced14296afb8"

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262 }

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263 ]

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264 },

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265 "6": {

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266 "annotation": "",

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267 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0",

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268 "id": 6,

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269 "input_connections": {

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270 "inputFile": {

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271 "id": 5,

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272 "output_name": "bam_output"

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273 }

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274 },

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275 "inputs": [],

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276 "label": null,

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277 "name": "FilterSamReads",

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278 "outputs": [

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279 {

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280 "name": "outFile",

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281 "type": "bam"

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282 }

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283 ],

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284 "position": {

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285 "left": 1028,

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286 "top": 200

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287 },

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288 "post_job_actions": {

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289 "DeleteIntermediatesActionoutFile": {

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290 "action_arguments": {},

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291 "action_type": "DeleteIntermediatesAction",

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292 "output_name": "outFile"

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293 }

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294 },

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295 "tool_errors": null,

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296 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0",

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297 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",

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298 "tool_version": "1.136.0",

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299 "type": "tool",

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300 "uuid": "bf824957-0907-4c1f-983d-f26a88826253",

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301 "workflow_outputs": [

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302 {

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303 "label": null,

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304 "output_name": "outFile",

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305 "uuid": "7aeb6a2f-a869-44df-bb2a-188e44036d1e"

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306 }

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307 ]

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308 },

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309 "7": {

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310 "annotation": "",

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311 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",

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312 "id": 7,

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313 "input_connections": {

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314 "input_type|bam_input": {

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315 "id": 6,

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316 "output_name": "outFile"

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317 },

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318 "reference_source|ref_file": {

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319 "id": 0,

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320 "output_name": "output"

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321 }

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322 },

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323 "inputs": [],

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324 "label": null,

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325 "name": "Map with BWA",

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326 "outputs": [

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327 {

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328 "name": "bam_output",

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329 "type": "bam"

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330 }

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331 ],

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332 "position": {

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333 "left": 1356,

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334 "top": 200

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335 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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336 "post_job_actions": {

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337 "DeleteIntermediatesActionbam_output": {

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338 "action_arguments": {},

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339 "action_type": "DeleteIntermediatesAction",

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340 "output_name": "bam_output"

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341 }

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342 },

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343 "tool_errors": null,

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344 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",

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345 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": null, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"__current_case__\\\": 3, \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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346 "tool_version": "0.7.12.1",

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347 "type": "tool",

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348 "uuid": "9d1d2fe9-c3c6-4a34-a28d-50b2f7a06e11",

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349 "workflow_outputs": [

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350 {

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351 "label": null,

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352 "output_name": "bam_output",

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353 "uuid": "981cdac9-e993-471c-87c2-c667431ed47f"

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354 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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355 ]

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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356 },

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357 "8": {

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358 "annotation": "",

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359 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1",

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360 "id": 8,

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361 "input_connections": {

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362 "inputFile": {

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363 "id": 7,

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364 "output_name": "bam_output"

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365 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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366 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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367 "inputs": [],

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368 "label": null,

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369 "name": "SortSam",

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370 "outputs": [

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371 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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372 "name": "outFile",

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373 "type": "bam"

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374 }

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375 ],

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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376 "position": {

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377 "left": 1621,

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378 "top": 200

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379 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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380 "post_job_actions": {

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381 "DeleteIntermediatesActionoutFile": {

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382 "action_arguments": {},

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383 "action_type": "DeleteIntermediatesAction",

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384 "output_name": "outFile"

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385 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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386 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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387 "tool_errors": null,

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388 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1",

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389 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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390 "tool_version": "1.136.1",

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391 "type": "tool",

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392 "uuid": "42d32394-d968-4cb0-ae06-69e551a8d328",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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393 "workflow_outputs": [

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394 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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395 "label": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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396 "output_name": "outFile",

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397 "uuid": "30ae35f3-4cda-4feb-bfbe-6005ea4dcd22"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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398 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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399 ]

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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400 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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401 "9": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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402 "annotation": "",

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403 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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404 "id": 9,

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405 "input_connections": {

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406 "input1": {

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407 "id": 8,

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408 "output_name": "outFile"

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409 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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410 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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411 "inputs": [],

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412 "label": null,

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413 "name": "BAM-to-SAM",

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414 "outputs": [

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415 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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416 "name": "output1",

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417 "type": "sam"

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418 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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419 ],

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

420 "position": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

421 "left": 1949,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

422 "top": 200

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

423 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

424 "post_job_actions": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

425 "DeleteIntermediatesActionoutput1": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

426 "action_arguments": {},

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

427 "action_type": "DeleteIntermediatesAction",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

428 "output_name": "output1"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

429 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

430 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

431 "tool_errors": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

432 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

433 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

434 "tool_version": "2.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

435 "type": "tool",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

436 "uuid": "9fe23b03-b221-4007-a406-44b05be85066",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

437 "workflow_outputs": [

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

438 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

439 "label": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

440 "output_name": "output1",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

441 "uuid": "c34f9ca8-8d2d-4d8a-bb24-c3a030ff45af"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

442 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

443 ]

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

444 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

445 "10": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

446 "annotation": "",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

447 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

448 "id": 10,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

449 "input_connections": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

450 "input1": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

451 "id": 0,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

452 "output_name": "output"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

453 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

454 "input2": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

455 "id": 9,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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diff changeset

456 "output_name": "output1"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

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diff changeset

457 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

458 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

459 "inputs": [],

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

460 "label": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

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diff changeset

461 "name": "Coverage Sampler",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

462 "outputs": [

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

463 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

464 "name": "output1",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

465 "type": "tabular"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

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diff changeset

466 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

467 ],

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

468 "position": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

469 "left": 2184,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

470 "top": 200

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

471 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

472 "post_job_actions": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

473 "RenameDatasetActionoutput1": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

474 "action_arguments": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

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diff changeset

475 "newname": "Coverage Results"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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diff changeset

476 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

477 "action_type": "RenameDatasetAction",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

478 "output_name": "output1"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

479 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

480 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

481 "tool_errors": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

482 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

483 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

484 "tool_version": "0.1.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

485 "type": "tool",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

486 "uuid": "8305b84c-ceb2-41bb-9f07-4c7bedff5d0a",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

487 "workflow_outputs": [

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

488 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

489 "label": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

490 "output_name": "output1",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

491 "uuid": "1db38476-e927-44aa-bac5-0ff46b81a2b7"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

492 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

493 ]

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

494 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

495 "11": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

496 "annotation": "",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

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parents:

diff changeset

497 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

498 "id": 11,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

499 "input_connections": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

500 "input1": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

501 "id": 0,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

502 "output_name": "output"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

503 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

504 "sam_type|sampe_input2": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

505 "id": 9,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

506 "output_name": "output1"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

507 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

508 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

509 "inputs": [],

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

510 "label": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

511 "name": "Snip Finder",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

512 "outputs": [

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

513 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

514 "name": "output1",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

515 "type": "tabular"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

516 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

517 ],

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

518 "position": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

519 "left": 2184,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

520 "top": 341

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

521 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

522 "post_job_actions": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

523 "RenameDatasetActionoutput1": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

524 "action_arguments": {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

525 "newname": "Snip Results"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

526 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

527 "action_type": "RenameDatasetAction",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

528 "output_name": "output1"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

529 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

530 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

531 "tool_errors": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

532 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

533 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"False\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

534 "tool_version": "0.1.0",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

535 "type": "tool",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

536 "uuid": "b7bac673-aed8-4abd-a873-f842b9497ac8",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

537 "workflow_outputs": [

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

538 {

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

539 "label": null,

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

540 "output_name": "output1",

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

541 "uuid": "fb7fbbba-05bd-4477-a0ee-8e51bcbeddd2"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

542 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

543 ]

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

544 }

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

545 },

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

546 "uuid": "6c6ee2ed-be38-4787-9a8e-5ab9a872a00e"

d1896971200b planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 9e86c4ae3eb19f5c493ac96f86c6235ab3df5368

chrisd

parents:

diff changeset

547 }

Mercurial > repos > chrisd > amrplusplus_workflow

annotate amrplusplus_pe.ga @ 4:d1896971200b draft