Merge pull request #485 from Proteobench/DIA-modules-documentation

update module documentation

docs/available-modules/2-DDA-Quantification-ion-level.md → docs/available-modules/2-quant-lfq-ion-dda.md

@@ -213,7 +213,7 @@ Example: when 3 is selected, only the precursor ions quantified in 3 or more raw
 
 To make the results available to the entire community, you need to provide the parameter file that corresponds to 
 your analysis. You can upload it in the drag and drop area in the "Add results to online repository" section (under Download calculated ratio's). 
-See [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-DDA-Quantification-ion-level/#important-tool-specific-settings)
+See [here](#important-tool-specific-settings)
 for all compatible parameter files.
 In this module, we keep track of the following parameters, if you feel 
 that some important information is missing, please add it in the 

docs/available-modules/3-DDA-Quantification-peptidoform-level.md → docs/available-modules/3-quant-lfq-peptidoform-dda.md

@@ -1,7 +1,7 @@
 # DDA quantification - peptidoforms
 
 This module compares the sensitivity and quantification accuracy for data acquired with data-dependent acquisition (DDA) on a Q Exactive HF-X Orbitrap (Thermo Fisher).
-It is based on the DDA quantification module "ion-level" described [here](https://proteobench.readthedocs.io/en/stable/available-modules/3-DDA-Quantification-peptidoform-level). Data and metrics are the same, the difference is that in this module we focus on peptidoform quantities summarised from the ion quantities. 
+It is based on the DDA quantification module "ion-level" described [here](#2-quant-lfq-ion-dda). Data and metrics are the same, the difference is that in this module we focus on peptidoform quantities summarised from the ion quantities. 
 
 ## How to use
 

docs/available-modules/4-DIA-Quantification.md → docs/available-modules/4-quant-lfq-ion-dia-aif.md

@@ -203,7 +203,7 @@ Example: when 3 is selected, only the precursor ions quantified in 3 or more raw
 
 To make the results available to the entire community, you need to provide the parameter file that corresponds to 
 your analysis. You can upload it in the drag and drop area in the "Add results to online repository" section (under Download calculated ratio's). 
-See [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-DDA-Quantification-ion-level/#important-tool-specific-settings)
+See [here](#important-tool-specific-settings)
 for all compatible parameter files.
 In this module, we keep track of the following parameters, if you feel 
 that some important information is missing, please add it in the 

docs/available-modules/5-quant-lfq-ion-dia-diapasef.md

@@ -0,0 +1,6 @@
+# DIA quantification - ion level - diaPASEF
+
+This module compares the sensitivity and quantification accuracy for data acquired with data-independent acquisition (DIA) on a timsTOF (Bruker).
+It is similar to the DIA quantification module "ion-level" described [here](#4-quant-lfq-ion-dia-aif).
+
+**We are working on the documentation: more information comming soon.**

webinterface/pages/markdown_files/Quant/lfq/ion/DDA/input_file_description.md

@@ -1,3 +1,3 @@
 
 Please upload the output of your analysis, and indicate what software
-tool it comes from (this is necessary to correctly parse your table - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/2-DDA-Quantification-ion-level/#how-to-use)" section of this module. For the data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/2-DDA-Quantification-ion-level/#data-set)". You can download an (*incomplete*) MaxQuant file example [here](https://raw.githubusercontent.com/Proteobench/ProteoBench/refs/heads/main/test/data/dda_quant/MaxQuant_2_5_1_evidence_sample.txt).
+tool it comes from (this is necessary to correctly parse your table - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/2-quant-lfq-ion-dda/#how-to-use)" section of this module. For the data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/2-quant-lfq-ion-dda/#data-set)". You can download an (*incomplete*) MaxQuant file example [here](https://raw.githubusercontent.com/Proteobench/ProteoBench/refs/heads/main/test/data/dda_quant/MaxQuant_2_5_1_evidence_sample.txt).

webinterface/pages/markdown_files/Quant/lfq/ion/DDA/introduction_DDA_quan_ions.md

@@ -17,4 +17,4 @@ ProteoBench plots these three metrics to visualize workflow outputs
     from different tools, with different versions, and/or different
 sets of parameters for the search and quantification.
 The full description of the pre-processing steps and metrics
-calculation is available [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-DDA-Quantification-ion-level/).
+calculation is available [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-quant-lfq-ion-dda/).

webinterface/pages/markdown_files/Quant/lfq/ion/DDA/submit_description.md

@@ -2,7 +2,7 @@
 
 To do so, you need to provide the parameter file that corresponds to 
 your analysis. You can upload it in the drag and drop area below. 
-See [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-DDA-Quantification-ion-level/)
+See [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-quant-lfq-ion-dda/)
 for all compatible parameter files.
 In this module, we keep track of the following parameters, if you feel 
 that some important information is missing, please add it in the 

webinterface/pages/markdown_files/Quant/lfq/ion/DIA/AIF/input_file_description.md

@@ -1,9 +1,9 @@
 Please upload the ouput of your analysis, and indicate what software 
 tool it comes from (this is necessary to correctly parse your table - find 
-more information in the "[How to use](https://proteobench.readthedocs.io/en/stable/available-modules/4-DIA-Quantification/)"
+more information in the "[How to use](https://proteobench.readthedocs.io/en/stable/available-modules/4-quant-lfq-ion-dia-aif/)"
 section of this module).
 
-Currently, we support output files from AlphaDIA, DIA-NN, FragPipe, MSAID, MaxQuant and Spectronaut. It is also possible to reformat your data in a tab-delimited file that we call "custom format" in the [documentation](https://proteobench.readthedocs.io/en/latest/available-modules/4-DIA-Quantification/). 
+Currently, we support output files from AlphaDIA, DIA-NN, FragPipe, MSAID, MaxQuant and Spectronaut. It is also possible to reformat your data in a tab-delimited file that we call "custom format" in the [documentation](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/). 
 
 Remember: contaminant sequences are already present in the fasta file 
 associated to this module. **Do not add other contaminants** to your 

webinterface/pages/markdown_files/Quant/lfq/ion/DIA/diaPASEF/input_file_description.md

@@ -1,9 +1,9 @@
 Please upload the ouput of your analysis, and indicate what software 
 tool it comes from (this is necessary to correctly parse your table - find 
-more information in the "[How to use](https://proteobench.readthedocs.io/en/stable/available-modules/4-DIA-Quantification/)"
+more information in the "[How to use](https://proteobench.readthedocs.io/en/stable/available-modules/4-quant-lfq-ion-dia-aif/)"
 section of this module).
 
-Currently, we support output files from AlphaDIA and DIA-NN. It is also possible to reformat your data in a tab-delimited file that we call "custom format" in the [documentation](https://proteobench.readthedocs.io/en/latest/available-modules/4-DIA-Quantification/). We are still working on EncyclopeDIA, MSFraggerDIA, Skyline and Spectronaut.
+Currently, we support output files from AlphaDIA and DIA-NN. It is also possible to reformat your data in a tab-delimited file that we call "custom format" in the [documentation](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/). We are still working on EncyclopeDIA, MSFraggerDIA, Skyline and Spectronaut.
 
 Remember: contaminant sequences are already present in the fasta file 
 associated to this module. **Do not add other contaminants** to your 

webinterface/pages/markdown_files/Quant/lfq/peptidoform/DDA/input_file_description.md

@@ -1,3 +1,3 @@
 
 Please upload the output of your analysis, and indicate what software
-tool it comes from (this is necessary to correctly parse your table - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/3-DDA-Quantification-peptidoform-level/#how-to-use)" section of this module. For the data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/3-DDA-Quantification-peptidoform-level/#data-set)".
+tool it comes from (this is necessary to correctly parse your table - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/3-quant-lfq-peptidoform-dda/#how-to-use)" section of this module. For the data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/3-quant-lfq-peptidoform-dda/#data-set)".

webinterface/pages/markdown_files/Quant/lfq/peptidoform/DDA/submit_description.md

@@ -2,7 +2,7 @@
 
 To do so, you need to provide the parameter file that corresponds to 
 your analysis. You can upload it in the drag and drop area below. 
-See [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-DDA-Quantification-ion-level/)
+See [here](https://proteobench.readthedocs.io/en/stable/available-modules/2-quant-lfq-ion-dda/)
 for all compatible parameter files.
 In this module, we keep track of the following parameters, if you feel 
 that some important information is missing, please add it in the 

webinterface/pages/texts/generic_texts.py

@@ -8,7 +8,7 @@ class ShortMessages:
 
         title = "DDA quantification - precursor ions"
 
-        doc_url = "https://proteobench.readthedocs.io/en/latest/available-modules/4-DIA-Quantification/"
+        doc_url = "https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/"
 
         initial_results = """
             Scroll down if you want to see the public benchmark runs publicly available
@@ -41,7 +41,7 @@ class ShortMessages:
     class Help:
         input_file = """
             Output file of the software tool. More information on the accepted format can 
-            be found [here](https://proteobench.readthedocs.io/en/latest/available-modules/4-DIA-Quantification/)
+            be found [here](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/)
             """
 
         pull_req = """
@@ -51,7 +51,7 @@ class Help:
         input_format = """
             Please select the software you used to generate the results. If it is not yet 
             implemented in ProteoBench, you can use a tab-delimited format that is described 
-            further [here](https://proteobench.readthedocs.io/en/latest/available-modules/4-DIA-Quantification/)
+            further [here](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/)
         """
 
         parse_button = """
@@ -60,6 +60,6 @@ class Help:
 
         meta_data_file = """
             Please add a file with meta data that contains all relevant information about 
-            your search parameters. See [here](https://proteobench.readthedocs.io/en/latest/available-modules/4-DIA-Quantification/)
+            your search parameters. See [here](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/)
             for all compatible parameter files.
         """