Mercurial > repos > nml > mob_suite
annotate workflows/AMRworkflow_STARAMR.ga @ 2:2c7f721a4905 draft
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
author | nml |
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date | Fri, 17 Aug 2018 11:12:08 -0400 |
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children | 066b2a1c6a55 |
rev | line source |
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2
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff
changeset
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1 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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2 "a_galaxy_workflow": "true", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff
changeset
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3 "annotation": "", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff
changeset
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4 "format-version": "0.1", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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5 "name": "AMRworkflow", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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6 "steps": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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7 "0": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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diff
changeset
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8 "annotation": "", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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9 "content_id": "mob_recon", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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10 "errors": null, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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11 "id": 0, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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12 "input_connections": {}, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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13 "inputs": [ |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
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14 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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15 "description": "runtime parameter for tool MOB-Recon", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
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16 "name": "input" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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17 } |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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18 ], |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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19 "label": null, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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20 "name": "MOB-Recon", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
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21 "outputs": [ |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
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22 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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23 "name": "seqhits", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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24 "type": "input" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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25 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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26 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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27 "name": "outfile1", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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28 "type": "tabular" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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29 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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30 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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31 "name": "outfile2", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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32 "type": "tabular" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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33 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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34 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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35 "name": "outfile3", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
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36 "type": "tabular" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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37 } |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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38 ], |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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39 "position": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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40 "left": 200, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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41 "top": 200 |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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42 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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43 "post_job_actions": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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44 "HideDatasetActionoutfile1": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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45 "action_arguments": {}, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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46 "action_type": "HideDatasetAction", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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47 "output_name": "outfile1" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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48 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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49 "HideDatasetActionoutfile2": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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50 "action_arguments": {}, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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51 "action_type": "HideDatasetAction", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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52 "output_name": "outfile2" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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53 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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54 "HideDatasetActionoutfile3": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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55 "action_arguments": {}, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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56 "action_type": "HideDatasetAction", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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57 "output_name": "outfile3" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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58 } |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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59 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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60 "tool_id": "mob_recon", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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61 "tool_state": "{\"adv_param\": \"{\\\"min_length_condition\\\": {\\\"min_length_param\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"min_con_ident\\\": \\\"80\\\", \\\"min_mob_ident\\\": \\\"80\\\", \\\"min_mob_evalue\\\": \\\"1e-05\\\", \\\"min_rep_evalue\\\": \\\"1e-05\\\", \\\"unicycler_contigs\\\": \\\"True\\\", \\\"min_rep_ident\\\": \\\"80\\\", \\\"min_rpp_evalue\\\": \\\"1e-05\\\", \\\"min_rpp_ident\\\": \\\"80\\\", \\\"run_circlator\\\": \\\"True\\\", \\\"min_con_evalue\\\": \\\"1e-05\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": null}", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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62 "tool_version": "1.4.8", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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63 "type": "tool", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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64 "uuid": "017d5861-8836-46a8-8444-0dcaca60eda1", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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65 "workflow_outputs": [ |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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66 { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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67 "label": null, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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68 "output_name": "seqhits", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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69 "uuid": "6304bc2b-bcc9-47c4-8e3b-9d2ee5a80433" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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70 } |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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71 ] |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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72 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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73 "1": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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74 "annotation": "", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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75 "content_id": "staramr_search", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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76 "errors": null, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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77 "id": 1, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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78 "input_connections": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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79 "genomes": { |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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80 "id": 0, |
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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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81 "output_name": "seqhits" |
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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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82 } |
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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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83 }, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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84 "inputs": [ |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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85 { |
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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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86 "description": "runtime parameter for tool staramr", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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87 "name": "genomes" |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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88 } |
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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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89 ], |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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90 "label": null, |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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91 "name": "staramr", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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92 "outputs": [ |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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93 { |
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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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94 "name": "blast_hits", |
2c7f721a4905
planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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95 "type": "input" |
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96 }, |
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97 { |
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98 "name": "summary", |
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99 "type": "tabular" |
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100 }, |
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101 { |
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102 "name": "resfinder", |
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103 "type": "tabular" |
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104 }, |
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105 { |
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106 "name": "pointfinder", |
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107 "type": "tabular" |
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108 }, |
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109 { |
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110 "name": "settings", |
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111 "type": "txt" |
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112 }, |
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113 { |
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114 "name": "excel", |
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115 "type": "xlsx" |
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116 } |
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117 ], |
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118 "position": { |
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119 "left": 420, |
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120 "top": 200 |
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121 }, |
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122 "post_job_actions": { |
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123 "HideDatasetActionpointfinder": { |
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124 "action_arguments": {}, |
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125 "action_type": "HideDatasetAction", |
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126 "output_name": "pointfinder" |
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127 }, |
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128 "HideDatasetActionsettings": { |
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129 "action_arguments": {}, |
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130 "action_type": "HideDatasetAction", |
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131 "output_name": "settings" |
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132 } |
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133 }, |
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134 "tool_id": "staramr_search", |
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135 "tool_state": "{\"__page__\": null, \"use_pointfinder\": \"{\\\"enable\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genomes\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"pid_threshold\\\": \\\"98.0\\\", \\\"exclude_resistance_phenotypes\\\": \\\"false\\\", \\\"exclude_negatives\\\": \\\"false\\\", \\\"plength_resfinder\\\": \\\"60.0\\\", \\\"plength_pointfinder\\\": \\\"95.0\\\", \\\"report_all_blast\\\": \\\"false\\\"}\"}", |
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136 "tool_version": "0.2.2", |
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137 "type": "tool", |
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138 "uuid": "41f8718f-87a0-45d2-b79d-e5afddea1532", |
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139 "workflow_outputs": [ |
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140 { |
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141 "label": null, |
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142 "output_name": "blast_hits", |
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143 "uuid": "9e8592ad-71c0-4528-8e8b-efcd3bb9183a" |
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144 }, |
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145 { |
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146 "label": null, |
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147 "output_name": "resfinder", |
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148 "uuid": "2f27a46b-29bf-4abf-9d26-fce4e9fc9dd5" |
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149 }, |
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150 { |
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151 "label": null, |
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152 "output_name": "excel", |
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153 "uuid": "67549d0b-0480-4c25-8bfd-1fa78cfdb066" |
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154 }, |
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155 { |
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156 "label": null, |
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157 "output_name": "summary", |
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158 "uuid": "17c9e48c-234a-4cb7-986d-f88166bfe0a7" |
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159 } |
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160 ] |
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161 } |
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162 }, |
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163 "tags": [], |
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164 "uuid": "4c695847-5fc7-4020-a125-a500700ab320" |
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165 } |