177177 ],
178178 "format-version": "0.1",
179179 "license": "MIT",
180- "release": "1.0beta6",
181180 "name": "PretextMap Generation from 1 or 2 haplotypes",
182181 "report": {
183182 "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
533532 "output_name": "output"
534533 }
535534 },
536- "inputs": [],
535+ "inputs": [
536+ {
537+ "description": "runtime parameter for tool Map parameter value",
538+ "name": "input_param_type"
539+ }
540+ ],
537541 "label": "Hap2 not provided",
538542 "name": "Map parameter value",
539543 "outputs": [
11131117 }
11141118 },
11151119 "tags": [],
1116- "uuid": "8fb65374-0776-4aa9-80d8-eb0b8c69f274 "
1120+ "uuid": "51b0f229-4332-49f4-99f0-662d684a40ff "
11171121 },
11181122 "tool_id": null,
11191123 "type": "subworkflow",
14581462 }
14591463 },
14601464 "tags": [],
1461- "uuid": "c32e34b2-4390-4bf2-9048-411280d63ddd "
1465+ "uuid": "ab0a1e42-dc07-4127-ba93-a46757bdbeef "
14621466 },
14631467 "tool_id": null,
14641468 "type": "subworkflow",
16941698 "output_name": "output"
16951699 }
16961700 },
1697- "inputs": [],
1701+ "inputs": [
1702+ {
1703+ "description": "runtime parameter for tool Cutadapt",
1704+ "name": "library"
1705+ }
1706+ ],
16981707 "label": "Trim Hi-C reads 2",
16991708 "name": "Cutadapt",
17001709 "outputs": [
18321841 "output_name": "output"
18331842 }
18341843 },
1835- "inputs": [],
1844+ "inputs": [
1845+ {
1846+ "description": "runtime parameter for tool BWA-MEM2",
1847+ "name": "fastq_input"
1848+ },
1849+ {
1850+ "description": "runtime parameter for tool BWA-MEM2",
1851+ "name": "reference_source"
1852+ }
1853+ ],
18361854 "label": null,
18371855 "name": "BWA-MEM2",
18381856 "outputs": [
18811899 },
18821900 "6": {
18831901 "annotation": "",
1884- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2 ",
1902+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0 ",
18851903 "errors": null,
18861904 "id": 6,
18871905 "input_connections": {
18901908 "output_name": "bam_output"
18911909 }
18921910 },
1893- "inputs": [],
1911+ "inputs": [
1912+ {
1913+ "description": "runtime parameter for tool Samtools merge",
1914+ "name": "bed_file"
1915+ },
1916+ {
1917+ "description": "runtime parameter for tool Samtools merge",
1918+ "name": "headerbam"
1919+ }
1920+ ],
18941921 "label": null,
18951922 "name": "Samtools merge",
18961923 "outputs": [
19121939 "output_name": "output"
19131940 }
19141941 },
1915- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2 ",
1942+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0 ",
19161943 "tool_shed_repository": {
1917- "changeset_revision": "cae2794d2deb ",
1944+ "changeset_revision": "a7617eb92baf ",
19181945 "name": "samtools_merge",
19191946 "owner": "iuc",
19201947 "tool_shed": "toolshed.g2.bx.psu.edu"
19211948 },
19221949 "tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
1923- "tool_version": "1.20+galaxy2 ",
1950+ "tool_version": "1.21+galaxy0 ",
19241951 "type": "tool",
19251952 "uuid": "f536be00-adc2-4f1f-a167-f3fd44466290",
19261953 "when": null,
19341961 }
19351962 },
19361963 "tags": [],
1937- "uuid": "52451b6f-5046-4926-b61e-a16cae121c1e "
1964+ "uuid": "e3480066-7c21-4216-ba4d-8e42dcfa3fa2 "
19381965 },
19391966 "tool_id": null,
19401967 "type": "subworkflow",
20922119 "output_name": "data_param"
20932120 }
20942121 },
2095- "inputs": [],
2122+ "inputs": [
2123+ {
2124+ "description": "runtime parameter for tool Map with minimap2",
2125+ "name": "fastq_input"
2126+ },
2127+ {
2128+ "description": "runtime parameter for tool Map with minimap2",
2129+ "name": "reference_source"
2130+ }
2131+ ],
20962132 "label": null,
20972133 "name": "Map with minimap2",
20982134 "outputs": [
21662202 },
21672203 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
21682204 "tool_shed_repository": {
2169- "changeset_revision": "c6cec5ab35c1 ",
2205+ "changeset_revision": "0346286a3b0a ",
21702206 "name": "pretext_map",
21712207 "owner": "iuc",
21722208 "tool_shed": "toolshed.g2.bx.psu.edu"
22222258 },
22232259 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
22242260 "tool_shed_repository": {
2225- "changeset_revision": "c6cec5ab35c1 ",
2261+ "changeset_revision": "0346286a3b0a ",
22262262 "name": "pretext_map",
22272263 "owner": "iuc",
22282264 "tool_shed": "toolshed.g2.bx.psu.edu"
24112447 "output_name": "alignment_output"
24122448 }
24132449 },
2414- "inputs": [],
2450+ "inputs": [
2451+ {
2452+ "description": "runtime parameter for tool bedtools Genome Coverage",
2453+ "name": "input_type"
2454+ }
2455+ ],
24152456 "label": null,
24162457 "name": "bedtools Genome Coverage",
24172458 "outputs": [
25492590 },
25502591 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
25512592 "tool_shed_repository": {
2552- "changeset_revision": "408ece2e4647 ",
2593+ "changeset_revision": "936a1edffce8 ",
25532594 "name": "pretext_graph",
25542595 "owner": "iuc",
25552596 "tool_shed": "toolshed.g2.bx.psu.edu"
25982639 },
25992640 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
26002641 "tool_shed_repository": {
2601- "changeset_revision": "408ece2e4647 ",
2642+ "changeset_revision": "936a1edffce8 ",
26022643 "name": "pretext_graph",
26032644 "owner": "iuc",
26042645 "tool_shed": "toolshed.g2.bx.psu.edu"
27662807 "output_name": "text_param"
27672808 }
27682809 },
2769- "inputs": [],
2810+ "inputs": [
2811+ {
2812+ "description": "runtime parameter for tool Map parameter value",
2813+ "name": "input_param_type"
2814+ }
2815+ ],
27702816 "label": "False if telomere track is empty",
27712817 "name": "Map parameter value",
27722818 "outputs": [
28412887 },
28422888 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
28432889 "tool_shed_repository": {
2844- "changeset_revision": "408ece2e4647 ",
2890+ "changeset_revision": "936a1edffce8 ",
28452891 "name": "pretext_graph",
28462892 "owner": "iuc",
28472893 "tool_shed": "toolshed.g2.bx.psu.edu"
28942940 },
28952941 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
28962942 "tool_shed_repository": {
2897- "changeset_revision": "408ece2e4647 ",
2943+ "changeset_revision": "936a1edffce8 ",
28982944 "name": "pretext_graph",
28992945 "owner": "iuc",
29002946 "tool_shed": "toolshed.g2.bx.psu.edu"
30413087 },
30423088 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
30433089 "tool_shed_repository": {
3044- "changeset_revision": "408ece2e4647 ",
3090+ "changeset_revision": "936a1edffce8 ",
30453091 "name": "pretext_graph",
30463092 "owner": "iuc",
30473093 "tool_shed": "toolshed.g2.bx.psu.edu"
30903136 },
30913137 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
30923138 "tool_shed_repository": {
3093- "changeset_revision": "408ece2e4647 ",
3139+ "changeset_revision": "936a1edffce8 ",
30943140 "name": "pretext_graph",
30953141 "owner": "iuc",
30963142 "tool_shed": "toolshed.g2.bx.psu.edu"
31483194 },
31493195 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
31503196 "tool_shed_repository": {
3151- "changeset_revision": "408ece2e4647 ",
3197+ "changeset_revision": "936a1edffce8 ",
31523198 "name": "pretext_graph",
31533199 "owner": "iuc",
31543200 "tool_shed": "toolshed.g2.bx.psu.edu"
32123258 },
32133259 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
32143260 "tool_shed_repository": {
3215- "changeset_revision": "408ece2e4647 ",
3261+ "changeset_revision": "936a1edffce8 ",
32163262 "name": "pretext_graph",
32173263 "owner": "iuc",
32183264 "tool_shed": "toolshed.g2.bx.psu.edu"
32323278 },
32333279 "41": {
32343280 "annotation": "",
3235- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4 +galaxy0",
3281+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5 +galaxy0",
32363282 "errors": null,
32373283 "id": 41,
32383284 "input_connections": {
32613307 "output_name": "pretext_snap_out"
32623308 }
32633309 },
3264- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4 +galaxy0",
3310+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5 +galaxy0",
32653311 "tool_shed_repository": {
3266- "changeset_revision": "26f2fe7e53a1 ",
3312+ "changeset_revision": "9ec9c22767c8 ",
32673313 "name": "pretext_snapshot",
32683314 "owner": "iuc",
32693315 "tool_shed": "toolshed.g2.bx.psu.edu"
32703316 },
32713317 "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"yes\", \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"2000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
3272- "tool_version": "0.0.4 +galaxy0",
3318+ "tool_version": "0.0.5 +galaxy0",
32733319 "type": "tool",
32743320 "uuid": "f453794e-4045-4602-9f49-26abf7f1426f",
32753321 "when": null,
32763322 "workflow_outputs": []
32773323 },
32783324 "42": {
32793325 "annotation": "",
3280- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4 +galaxy0",
3326+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5 +galaxy0",
32813327 "errors": null,
32823328 "id": 42,
32833329 "input_connections": {
33063352 "output_name": "pretext_snap_out"
33073353 }
33083354 },
3309- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4 +galaxy0",
3355+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5 +galaxy0",
33103356 "tool_shed_repository": {
3311- "changeset_revision": "26f2fe7e53a1 ",
3357+ "changeset_revision": "9ec9c22767c8 ",
33123358 "name": "pretext_snapshot",
33133359 "owner": "iuc",
33143360 "tool_shed": "toolshed.g2.bx.psu.edu"
33153361 },
33163362 "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"yes\", \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"2000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
3317- "tool_version": "0.0.4 +galaxy0",
3363+ "tool_version": "0.0.5 +galaxy0",
33183364 "type": "tool",
33193365 "uuid": "533b33d8-3a3b-480a-9978-1526d65606c5",
33203366 "when": null,
34303476 }
34313477 },
34323478 "tags": [],
3433- "uuid": "34226708-cba3-421c-809f-6ba105b3812c",
3434- "version": 4
3479+ "uuid": "97a25739-1f36-47ac-ba73-e529357f8528",
3480+ "version": 1,
3481+ "release": "1.0b7"
34353482}
0 commit comments