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Updating workflows/metabomics/lcms-preprocessing from 1.1 to 1.2
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planemo-autoupdate committed Feb 5, 2024
1 parent 765d714 commit f0c5b1e
Showing 1 changed file with 91 additions and 16 deletions.
107 changes: 91 additions & 16 deletions workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga
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Original file line number Diff line number Diff line change
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],
"format-version": "0.1",
"license": "MIT",
"release": "1.1",
"release": "1.2",
"name": "Mass spectrometry: LC-MS preprocessing with XCMS",
"steps": {
"0": {
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool MSnbase readMSData",
"name": "input"
}
],
"label": null,
"name": "MSnbase readMSData",
"outputs": [
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms plot chromatogram",
"name": "images"
},
{
"description": "runtime parameter for tool xcms plot chromatogram",
"name": "sampleMetadata"
}
],
"label": null,
"name": "xcms plot chromatogram",
"outputs": [
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"output_name": "xsetRData"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms findChromPeaks (xcmsSet)",
"name": "image"
}
],
"label": null,
"name": "xcms findChromPeaks (xcmsSet)",
"outputs": [
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms findChromPeaks Merger",
"name": "images"
},
{
"description": "runtime parameter for tool xcms findChromPeaks Merger",
"name": "sampleMetadata"
}
],
"label": null,
"name": "xcms findChromPeaks Merger",
"outputs": [
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"output_name": "xsetRData"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms groupChromPeaks (group)",
"name": "image"
}
],
"label": null,
"name": "xcms groupChromPeaks (group)",
"outputs": [
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"output_name": "xsetRData"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms adjustRtime (retcor)",
"name": "image"
}
],
"label": null,
"name": "xcms adjustRtime (retcor)",
"outputs": [
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},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8",
"content_id": "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.3.0",
"errors": null,
"id": 8,
"input_connections": {
Expand All @@ -376,7 +414,20 @@
"output_name": "variableMetadata"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Intensity Check",
"name": "dataMatrix_in"
},
{
"description": "runtime parameter for tool Intensity Check",
"name": "sampleMetadata_in"
},
{
"description": "runtime parameter for tool Intensity Check",
"name": "variableMetadata_in"
}
],
"label": null,
"name": "Intensity Check",
"outputs": [
Expand All @@ -394,15 +445,15 @@
"top": 495
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8",
"tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.3.0",
"tool_shed_repository": {
"changeset_revision": "a31f3f802b2b",
"changeset_revision": "ec75de7f1e08",
"name": "intensity_checks",
"owner": "melpetera",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/shared/mfs/data/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"dataMatrix_in\": {\"__class__\": \"ConnectedValue\"}, \"method_cond\": {\"method\": \"each_class\", \"__current_case__\": 1, \"class_col\": \"2\", \"chosen_stat\": [\"NA\"], \"test_fold_cond\": {\"test_fold\": \"No\", \"__current_case__\": 1}}, \"sampleMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"variableMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.2.8",
"tool_version": "1.3.0",
"type": "tool",
"uuid": "fcbec34b-b0d1-4d09-9873-a3c9c95399dc",
"when": null,
Expand All @@ -429,7 +480,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms plot chromatogram",
"name": "images"
},
{
"description": "runtime parameter for tool xcms plot chromatogram",
"name": "sampleMetadata"
}
],
"label": null,
"name": "xcms plot chromatogram",
"outputs": [
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"output_name": "xsetRData"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms groupChromPeaks (group)",
"name": "image"
}
],
"label": null,
"name": "xcms groupChromPeaks (group)",
"outputs": [
Expand Down Expand Up @@ -540,7 +605,12 @@
"output_name": "xsetRData"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool xcms fillChromPeaks (fillPeaks)",
"name": "image"
}
],
"label": null,
"name": "xcms fillChromPeaks (fillPeaks)",
"outputs": [
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"output_name": "xsetRData"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool CAMERA.annotate",
"name": "image"
}
],
"label": null,
"name": "CAMERA.annotate",
"outputs": [
Expand Down

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