# HG changeset patch
# User iuc
# Date 1688709066 0
# Node ID 1f89eeba299a7777bb424e3d78ac2d7ada29a96d
# Parent  0ceb9fb0f4cea4a69266cdb0111c812cb53d2d91
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5

diff -r 0ceb9fb0f4ce -r 1f89eeba299a freyja_aggregate_plot.xml
--- a/freyja_aggregate_plot.xml	Thu Jul 28 09:25:04 2022 +0000
+++ b/freyja_aggregate_plot.xml	Fri Jul 07 05:51:06 2023 +0000
@@ -71,6 +71,8 @@
                     </when>
                     <when value="no"/>
                 </conditional>
+                <expand macro="plot_lineages"/>
+                <expand macro="plot_mincov"/>
             </when>
             <when value="dash">
                 <param name="csv_meta" type="data" format="csv"
@@ -78,6 +80,7 @@
                        help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
                 <param name="plot_title" type="text" value="" optional="true" label="Title"/>
                 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"/>
+                <expand macro="plot_mincov"/>
             </when>
             <when value="plot_and_dash">
                 <param name="csv_meta" type="data" format="csv"
@@ -92,6 +95,8 @@
                     <option value="MS" selected="true">month bins</option>
                     <option value="D">day bins</option>
                 </param>
+                <expand macro="plot_lineages"/>
+                <expand macro="plot_mincov"/>
             </when>
             <when value="none"/>
         </conditional>
@@ -131,6 +136,7 @@
             </conditional>
             <output name="aggregated" ftype="tabular">
                 <assert_contents>
+                    <has_n_columns n="6" />
                     <has_text text="summarized"/>
                     <has_text text="abundances"/>
                     <has_text text="B.1.617.2"/>
@@ -148,6 +154,7 @@
                 <param name="csv_meta" value="csv_sample_meta.csv"/>
                 <param name="plot_title" value="This is title"/>
                 <param name="plot_intro" value="Local WW Dashboard"/>
+                <param name="mincov" value="75"/>
             </conditional>
             <output name="abundances_dashboard" ftype="html">
                 <assert_contents>
@@ -169,6 +176,7 @@
                     <param name="interval" value="D"/>
                 </conditional>
             </conditional>
+            <param name="lineages" value="true"/>
             <output name="abundances_plot" ftype="pdf">
                 <assert_contents>
                     <has_text text="Matplotlib"/>
@@ -184,19 +192,18 @@
             <conditional name="plot_format">
                 <param name="choice" value="dash"/>
                 <param name="csv_meta" value="csv_sample_meta2.csv"/>
-                <param name="plot_title" value="This is title"/>
-                <param name="plot_intro" value="Local WW Dashboard"/>
+                <param name="plot_title" value="Title"/>
+                <param name="plot_intro" value="Dashboard"/>
             </conditional>
             <output name="aggregated" ftype="tabular">
                 <assert_contents>
+                    <has_n_columns n="6" />
                     <has_text text="summarized"/>
-                    <has_text text="abundances"/>
-                    <has_text text="B.1.617.2"/>
                 </assert_contents>
             </output>
             <output name="abundances_dashboard" ftype="html">
                 <assert_contents>
-                    <has_text text="Local WW Dashboard"/>
+                    <has_text text="Dashboard"/>
                 </assert_contents>
             </output>
         </test>
@@ -216,6 +223,7 @@
             </conditional>
             <output name="aggregated" ftype="tabular">
                 <assert_contents>
+                    <has_n_columns n="6" />
                     <has_text text="summarized"/>
                     <has_text text="abundances"/>
                     <has_text text="B.1.617.2"/>
@@ -236,15 +244,14 @@
             <conditional name="plot_format">
                 <param name="choice" value="plot_and_dash"/>
                 <param name="csv_meta" value="csv_sample_meta2.csv"/>
-                <param name="plot_title" value="This is title"/>
-                <param name="plot_intro" value="Local WW Dashboard"/>
+                <param name="plot_title" value="Title"/>
+                <param name="plot_intro" value="Dashboard"/>
                 <param name="interval" value="D"/>
             </conditional>
             <output name="aggregated" ftype="tabular">
                 <assert_contents>
+                    <has_n_columns n="6" />
                     <has_text text="summarized"/>
-                    <has_text text="abundances"/>
-                    <has_text text="B.1.617.2"/>
                 </assert_contents>
             </output>
             <output name="abundances_plot" ftype="pdf">
@@ -254,7 +261,7 @@
             </output>
             <output name="abundances_dashboard" ftype="html">
                 <assert_contents>
-                    <has_text text="Local WW Dashboard"/>
+                    <has_text text="Dash"/>
                 </assert_contents>
             </output>
         </test>
@@ -265,7 +272,7 @@
 Information about **freyja aggregate** method
 =============================================
 
-Method for manipulating the "demixed" output files. 
+Method for manipulating the "demixed" output files.
 
 Outputs
 -------
@@ -277,33 +284,28 @@
 
 Method provides a fractional abundance estimate for all aggregated samples.
 
-A **time(s) metadata CSV file** should have this form:
+A **time(s) metadata CSV file** should have *Sample,sample_collection_datetime* form:
 
-*Sample,sample_collection_datetime*  
-
-*sample_0.tsv,03/01/21*  
+*sample_0.tsv,03/01/21*
 
-*sample_1.tsv,03/03/21*  
- 
-*sample_2.tsv,03/08/21*  
+*sample_1.tsv,03/03/21*
 
-*sample_3.tsv,03/10/21*  
+*sample_2.tsv,03/08/21*
 
-*sample_4.tsv,03/12/21*  
+*sample_3.tsv,03/10/21*
 
-*sample_5.tsv,03/14/21*  
+or *Sample,sample_collection_datetime,viral_load* form:
 
-*sample_6.tsv,03/17/21*  
+*sample_0.tsv,03/01/21,460326*
 
-*sample_7.tsv,03/20/21*  
+*sample_1.tsv,03/03/21,176645.1*
 
-*sample_8.tsv,03/25/21*  
-
-*sample_9.tsv,03/30/21*  
+*sample_2.tsv,03/08/21,449891.7*
 
-*sample_10.tsv,03/31/21*  
+*sample_3.tsv,03/10/21,361699.5*
 
-*sample_11.tsv,04/04/21*
+
+Note: sample_collection_datetime can have either *MM/DD/YY* or *YYYY-MM-DD* format.
 
 
 Information about **freyja dash** method
@@ -313,31 +315,18 @@
 
 A **sample(s) metadata CSV file** should have this form:
 
-*Sample,sample_collection_datetime,viral_load*  
-
-*sample_0.tsv,03/01/21,460326*  
-
-*sample_1.tsv,03/03/21,176645.1*  
+*Sample,sample_collection_datetime,viral_load*
 
-*sample_2.tsv,03/08/21,449891.7*  
+*sample_0.tsv,03/01/21,460326*
 
-*sample_3.tsv,03/10/21,361699.5*  
-
-*sample_4.tsv,03/12/21,658923.9*  
+*sample_1.tsv,03/03/21,176645.1*
 
-*sample_5.tsv,03/14/21,500432.8*  
-
-*sample_6.tsv,03/17/21,791406.4*  
-
-*sample_7.tsv,03/20/21,628119.9*  
+*sample_2.tsv,03/08/21,449891.7*
 
-*sample_8.tsv,03/25/21,810673.9*  
-
-*sample_9.tsv,03/30/21,1263564.4*  
+*sample_3.tsv,03/10/21,361699.5*
 
-*sample_10.tsv,03/31/21,1627556.3*  
 
-*sample_11.tsv,04/04/21,1528006.4*
+Note: sample_collection_datetime can have either *MM/DD/YY* or *YYYY-MM-DD* format.
 
 
     ]]></help>
diff -r 0ceb9fb0f4ce -r 1f89eeba299a macros.xml
--- a/macros.xml	Thu Jul 28 09:25:04 2022 +0000
+++ b/macros.xml	Fri Jul 07 05:51:06 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.3.8</token>
+    <token name="@TOOL_VERSION@">1.4.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -49,6 +49,7 @@
 echo '${plot_format.plot_title}' > plot_title.txt &&
 echo '${plot_format.plot_intro}' > plot_intro.txt &&
 freyja dash
+    --mincov $plot_format.mincov
     #if $need_aggregation.choice == 'no'
         '$tsv_aggregated'
     #else
@@ -61,6 +62,8 @@
 ]]></token>
     <token name="@PLOT_COMMAND@"><![CDATA[
 freyja plot
+    $plot_format.lineages
+    --mincov $plot_format.mincov
     #if $need_aggregation.choice == 'no'
         '$tsv_aggregated'
     #else
@@ -82,6 +85,8 @@
     @DASH_COMMAND@
 #else if $plot_format.choice == 'plot'
     freyja plot
+    $plot_format.lineages
+    --mincov $plot_format.mincov
     #if $need_aggregation.choice == 'no'
         $tsv_aggregated
     #else
@@ -129,6 +134,19 @@
                checked="false"
                label="Remove unconfirmed lineages from the analysis"
                help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
+        <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
+               checked="false"
+               label="Use larger library with non-public lineages"
+               help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
+    </xml>
+    <xml name="plot_lineages">
+        <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
+               checked="false" label="Use lineage specific breakdown"/>
+    </xml>
+    <xml name="plot_mincov">
+        <param argument="--mincov" type="float" min="0" max="100" value="60"
+               label="Minimum genome coverage"
+               help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/>
     </xml>
     <token name="@HELP_HEADER@"><![CDATA[
 What it does
@@ -145,7 +163,7 @@
 ]]></token>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.5281/zenodo.6585067</citation>
+            <citation type="doi">10.1038/s41586-022-05049-6</citation>
         </citations>
     </xml>
 </macros>