Edit lipid documentation

docs/README_LCMS_LIPID.md

@@ -1,9 +1,6 @@
 # Lipidomics Workflow (v1.0.0)
 
-<figure>
-<img src="metamsworkflow.png" alt="metamsworkflow.png" />
-<figcaption>image</figcaption>
-</figure>
+![](metamsworkflow.png)
 
 #TODO KRH: replace with lipid diagram when available
 
@@ -76,7 +73,6 @@ workflow does not use retention time scoring.
     <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
 -   Example Scan Translator file (applicable to the example dataset):
     <https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_scan_translator.toml>
 
@@ -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 \[MetabRef
-        documentation\] (<https://metabref.emsl.pnnl.gov/api>) for how
-        to generate a token.
+    -   MetabRef configuration key (metabref.token). See MetabRef
+        documentation (<https://metabref.emsl.pnnl.gov/api>) 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
 

docs/index_lipid.html

@@ -1,7 +1,6 @@
 <h1 id="lipidomics-workflow-v1.0.0">Lipidomics Workflow (v1.0.0)</h1>
 <figure>
 <img src="metamsworkflow.png" alt="metamsworkflow.png" />
-<figcaption>image</figcaption>
 </figure>
 <p>#TODO KRH: replace with lipid diagram when available</p>
 <h2 id="overview">Overview</h2>
@@ -61,16 +60,15 @@ <h2 id="test-datasets">Test datasets</h2>
 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</a></li>
 <li>Example CoreMS Parameter file (applicable to the example dataset):
 <a
-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</a>
-#TODO KRH: still needs to be uploaded</li>
+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</a></li>
 <li>Example Scan Translator file (applicable to the example dataset): <a
 href="https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_scan_translator.toml">https://nmdcdemo.emsl.pnnl.gov/lipidomics/parameter_files/emsl_lipidomics_scan_translator.toml</a></li>
 </ul>
 <h2 id="execution-details">Execution Details</h2>
 <p>This workflow should be executed using the wdl file provided in the
 MetaMS package (wdl/metaMS_lipidomics.wdl).</p>
 <p>Example command to run the workflow:</p>
-<pre><code>miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files</code></pre>
+<pre><code>miniwdl run wdl/metaMS_lipidomics.wdl -i metams_input_lipidomics.json --verbose --no-cache --copy-input-files</code></pre>
 <h3 id="inputs">Inputs</h3>
 <p>To use the wdl, inputs should be specified in a json file. See
 example input json file in wdl/metaMS_lipidomics.wdl.</p>
@@ -86,8 +84,8 @@ <h3 id="inputs">Inputs</h3>
 <ul>
 <li>CoreMS Parameter file (.toml)</li>
 <li>Scan Translator Parameter file (.toml)</li>
-<li>MetabRef configuration key (metabref.token). See [MetabRef
-documentation] (<a
+<li>MetabRef configuration key (metabref.token). See MetabRef
+documentation (<a
 href="https://metabref.emsl.pnnl.gov/api">https://metabref.emsl.pnnl.gov/api</a>)
 for how to generate a token.</li>
 </ul></li>
@@ -114,7 +112,7 @@ <h3 id="outputs">Outputs</h3>
 <h2 id="version-history">Version History</h2>
 <ul>
 <li>v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update
-wtih releease date when available</li>
+wtih release date when available</li>
 </ul>
 <h2 id="point-of-contact">Point of contact</h2>
 <p>Package maintainer: Katherine R. Heal &lt;<a

docs/index_lipid.rst

@@ -2,9 +2,7 @@ Lipidomics Workflow (v1.0.0)
 ============================
 
 .. figure:: metamsworkflow.png
-   :alt: image
-
-   image
+   :alt: diagram of lipid workflow
 
 #TODO KRH: replace with lipid diagram when available
 
@@ -73,7 +71,7 @@ Test datasets
 -------------
 
 - An example dataset can be downloaded from here: 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
+- Example CoreMS Parameter file (applicable to the example dataset): 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
 
 Execution Details
@@ -86,7 +84,7 @@ Example command to run the workflow:
 
 .. code-block::
 
-    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
 ~~~~~~
@@ -102,7 +100,7 @@ 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] (https://metabref.emsl.pnnl.gov/api) for how to generate a token.
+   -  MetabRef configuration key (metabref.token). See MetabRef documentation (https://metabref.emsl.pnnl.gov/api) for how to generate a token.
 -  Cores (optional input)
    -  How many cores to use for processing. Default is 1.
 
@@ -120,7 +118,7 @@ Outputs
 Version History
 ---------------
 
-- v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update wtih releease date when available
+- v1.0.0: Initial release of the lipidomics workflow #TODO KRH: update wtih release date when available
 
 Point of contact
 ----------------

requirements-dev.txt

@@ -5,4 +5,4 @@ pyprof2calltree
 memory_profiler
 twine
 bumpversion
-pypandoc
+pandoc