Added argsoap with custom db to doc

docs/source/index.md

@@ -60,6 +60,7 @@ walkthrough/tutorial
 
 tips/suggestions
 tips/faq
+tips/toolcustomdb
 ```
 
 ```{toctree}

docs/source/introduction.md

@@ -28,16 +28,17 @@ The full tree of dependencies among all modules is shown here.
 To summarise, the dependency tree has to be considered when ignoring specific modules, as they may inadvertently block other modules in the current or the next stream of analysis.
 
 <style type="text/css">
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+.tg  {border-collapse:collapse;border-color:#9ABAD9;border-spacing:0;}
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 .tg .tg-9wq8{border-color:inherit;text-align:center;vertical-align:middle}
+.tg .tg-9tkk{border-color:#9abad9;text-align:center;vertical-align:middle}
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+@media screen and (max-width: 767px) {.tg {width: auto !important;}.tg col {width: auto !important;}.tg-wrap {overflow-x: auto;-webkit-overflow-scrolling: touch;}}</style>
 <div class="tg-wrap"><table class="tg"><thead>
   <tr>
     <th class="tg-njus">Stream-level</th>
@@ -46,7 +47,7 @@ To summarise, the dependency tree has to be considered when ignoring specific mo
   </tr></thead>
 <tbody>
   <tr>
-    <td class="tg-uzvj" rowspan="7">Read-based</td>
+    <td class="tg-uzvj" rowspan="8">Read-based</td>
     <td class="tg-9wq8" rowspan="3">Pre Processing</td>
     <td class="tg-9wq8">fastp</td>
   </tr>
@@ -61,7 +62,10 @@ To summarise, the dependency tree has to be considered when ignoring specific mo
     <td class="tg-9wq8">fastqc + reads count</td>
   </tr>
   <tr>
-    <td class="tg-9wq8">Functional Annotation</td>
+    <td class="tg-9tkk" rowspan="2">Functional Annotation</td>
+    <td class="tg-9tkk">ARGs-OAP with Custom DB</td>
+  </tr>
+  <tr>
     <td class="tg-9wq8">mi-faser</td>
   </tr>
   <tr>
@@ -72,7 +76,7 @@ To summarise, the dependency tree has to be considered when ignoring specific mo
     <td class="tg-9wq8">metaPhlAn</td>
   </tr>
   <tr>
-    <td class="tg-uzvj" rowspan="16">Assembly-Based</td>
+    <td class="tg-uzvj" rowspan="16">Assembly Based</td>
     <td class="tg-9wq8" rowspan="2">Assembly</td>
     <td class="tg-9wq8">metaSPAdes</td>
   </tr>
@@ -131,7 +135,7 @@ To summarise, the dependency tree has to be considered when ignoring specific mo
     <td class="tg-9wq8">Bakta</td>
   </tr>
   <tr>
-    <td class="tg-uzvj" rowspan="12">Binning-Based</td>
+    <td class="tg-uzvj" rowspan="12">Binning Based</td>
     <td class="tg-9wq8">Binning</td>
     <td class="tg-9wq8">Multi-Binners (Metabat2 + MaxBin2 + SemiBin2)</td>
   </tr>

docs/source/tips/toolcustomdb.md

@@ -0,0 +1,38 @@
+# Tools with custom database
+
+In this page you will find some suggestion on how to setup custom db for specific tools.
+
+<br>
+
+## ARGs-OAP with Custom DB
+
+(Module: `func_classification_rb`)
+
+For detailed documentation, please refer to the ARGs-OAP Repository: [https://github.com/xinehc/args_oap](https://github.com/xinehc/args_oap)
+
+I will try to simplify based also on my experience using this tool. Moreover some checks will be performed on the provided files to avoid later issues with the code. 
+
+You need two files:
+
+- A fasta file of protein sequences, named for example `sequences.fasta` (Do not put space in the filename).
+We suggest to make this file as simple as possible. The header of each sequence should contain just the ID without any space, tab, or other irregular characters such as forward slash.
+Avoid duplicated headers and duplicated sequences.
+
+```
+>id1
+DQEATRFKT...
+>id2
+GWTRCMDCQ...
+```
+
+
+- A file named `mapping.tsv`, which is tab-separated. 
+This file should contain at least one column, describing all the IDs of the fasta sequences. 
+However you can put more columns, each one representing Class, Subclass or categories of your interests.
+Do not put space in the column name. We suggest putting "_" instead of spaces. Geomosaic will make some checks.
+
+```
+IDs    Class    Subclass    Metal_Resistances
+id1    class1    subclass1    iron
+id2    class2    subclass2    iron
+```