From c5d7cea1b7688381f4b7e3311d3635bbcb52a134 Mon Sep 17 00:00:00 2001 From: Katherine Heal Date: Thu, 12 Dec 2024 15:07:36 -0800 Subject: [PATCH] Edit lipid documentation --- docs/README_LCMS_LIPID.md | 16 ++++++---------- docs/index_lipid.html | 12 +++++------- docs/index_lipid.rst | 12 +++++------- requirements-dev.txt | 2 +- 4 files changed, 17 insertions(+), 25 deletions(-) diff --git a/docs/README_LCMS_LIPID.md b/docs/README_LCMS_LIPID.md index 3cf1019..b7f5157 100644 --- a/docs/README_LCMS_LIPID.md +++ b/docs/README_LCMS_LIPID.md @@ -1,9 +1,6 @@ # Lipidomics Workflow (v1.0.0) -
-metamsworkflow.png -
image
-
+![](metamsworkflow.png) #TODO KRH: replace with lipid diagram when available @@ -76,7 +73,6 @@ workflow does not use retention time scoring. - Example CoreMS Parameter file (applicable to the example dataset): - #TODO KRH: still needs to be uploaded - Example Scan Translator file (applicable to the example dataset): @@ -88,7 +84,7 @@ MetaMS package (wdl/metaMS_lipidomics.wdl). Example command to run the workflow: ``` -miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files +miniwdl run wdl/metaMS_lipidomics.wdl -i metams_input_lipidomics.json --verbose --no-cache --copy-input-files ``` ### Inputs @@ -104,9 +100,9 @@ The following inputs are required (declared in the input json file): - Workflow inputs - CoreMS Parameter file (.toml) - Scan Translator Parameter file (.toml) - - MetabRef configuration key (metabref.token). See \[MetabRef - documentation\] () for how - to generate a token. + - MetabRef configuration key (metabref.token). See MetabRef + documentation () for how to + generate a token. - Cores (optional input) - How many cores to use for processing. Default is 1. @@ -124,7 +120,7 @@ The following inputs are required (declared in the input json file): ## Version History - v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update - wtih releease date when available + wtih release date when available ## Point of contact diff --git a/docs/index_lipid.html b/docs/index_lipid.html index 950df1a..f2d2276 100644 --- a/docs/index_lipid.html +++ b/docs/index_lipid.html @@ -1,7 +1,6 @@

Lipidomics Workflow (v1.0.0)

metamsworkflow.png -
image

#TODO KRH: replace with lipid diagram when available

Overview

@@ -61,8 +60,7 @@

Test datasets

href="https://nmdcdemo.emsl.pnnl.gov/lipidomics/blanchard_11_8ws97026/Blanch_Nat_Lip_H_32_AB_O_19_NEG_25Jan18_Brandi-WCSH5801.raw">https://nmdcdemo.emsl.pnnl.gov/lipidomics/blanchard_11_8ws97026/Blanch_Nat_Lip_H_32_AB_O_19_NEG_25Jan18_Brandi-WCSH5801.raw
  • Example CoreMS Parameter file (applicable to the example dataset): https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_corems_params.toml -#TODO KRH: still needs to be uploaded
    • +href="https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_corems_params.toml">https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_corems_params.toml
  • Example Scan Translator file (applicable to the example dataset): https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_scan_translator.toml
    • @@ -70,7 +68,7 @@

    Execution Details

    This workflow should be executed using the wdl file provided in the MetaMS package (wdl/metaMS_lipidomics.wdl).

    Example command to run the workflow:

    -
    miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
    +
    miniwdl run wdl/metaMS_lipidomics.wdl -i metams_input_lipidomics.json --verbose --no-cache --copy-input-files

    Inputs

    To use the wdl, inputs should be specified in a json file. See example input json file in wdl/metaMS_lipidomics.wdl.

    @@ -86,8 +84,8 @@

    Inputs

    @@ -114,7 +112,7 @@

    Outputs

    Version History

    • v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update -wtih releease date when available
      • +wtih release date when available

    Point of contact

    Package maintainer: Katherine R. Heal <