--- a/plotly_blast_tool/plotlyblast.xml	Tue Jul 25 05:36:54 2023 +0000
+++ b/plotly_blast_tool/plotlyblast.xml	Wed Jul 26 06:35:18 2023 +0000
@@ -1,10 +1,10 @@
 <tool name="plotlyblast" id="plotlyblast" version="3.0">
-  <!--Source in git at: https://github.com/fubar2/galaxy-->
-  <!--Created by toolfactory@galaxy.org at 25/07/2023 14:13:15 using the Galaxy Tool Factory.-->
+  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
+  <!--Created by toolfactory@galaxy.org at 26/07/2023 15:45:12 using the Galaxy Tool Factory.-->
   <description>Plotly plot generator</description>
   <requirements>
-    <requirement type="package" version="1.5.3">pandas</requirement>
-    <requirement type="package" version="5.9.0">plotly</requirement>
+    <requirement type="package">pandas</requirement>
+    <requirement type="package">plotly</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" level="fatal"/>
@@ -52,7 +52,7 @@
 args = parser.parse_args()
 df = pd.read_csv(args.input_tab, sep='\t')
 NCOLS = df.columns.size
-MAXLEN = 40 # tricky way to truncate long axis tickmarks
+MAXLEN = 30 # tricky way to truncate long axis tickmarks
 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
 if len(args.header.strip()) > 0:
     newcols = args.header.split(',')
@@ -63,29 +63,34 @@
         df.columns = defaultcols
 else:
     df.columns = defaultcols
-df['evalue'] = [-math.log(x) for x in df['evalue']] # convert so large values reflect statistical surprise
+df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise
 if len(args.colourcol.strip()) == 0:
     fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
 else:
     fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
 if args.title:
-    ftitle=dict(text=args.title, font=dict(size=50))
+    ftitle=dict(text=args.title, font=dict(size=40), automargin=True)
     fig.update_layout(title=ftitle)
 for scatter in fig.data:
     scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
     scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
+    if len(args.colourcol.strip()) == 0:
+        sl = str(scatter['legendgroup'])
+        if len(sl) > MAXLEN:
+            scatter['legendgroup'] = sl[:MAXLEN]
 fig.write_html(args.htmlout)
 
+
 #end raw]]></configfile>
   </configfiles>
   <inputs>
     <param name="input_tab" type="data" optional="false" label="Tabular input file to plot" help="" format="tabular" multiple="false"/>
-    <param name="xcol" type="text" value="mismatch" label="x axis for plat" help=""/>
+    <param name="xcol" type="text" value="qaccver" label="x axis for plat" help=""/>
     <param name="ycol" type="text" value="bitscore" label="y axis for plot" help=""/>
-    <param name="colourcol" type="text" value="qaccver" label="column containing a groupable variable for colour. Default none." help="Adds a legend so choose wisely "/>
+    <param name="colourcol" type="text" value="piden" label="column containing a groupable variable for colour. Default none." help="Adds a legend so choose wisely "/>
     <param name="hovercol" type="text" value="qseq" label="columname for hover string" help=""/>
-    <param name="title" type="text" value="Test title default" label="Title for the plot" help=""/>
-    <param name="header" type="text" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" label="Use this comma delimited list of column header names for this tabular file__sq__s columns" help="Default for Galaxy blast outputs with 25 columns."/>
+    <param name="title" type="text" value="Qaccver by bitscore coloured by pident. Hover shows blast match." label="Title for the plot" help="Special characters will probably be escaped so do not use them"/>
+    <param name="header" type="text" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" label="Use this comma delimited list of column header names for this tabular file. Default is None when col1...coln will be used" help="Default for Galaxy blast outputs with 25 columns. The column names supplied for xcol, ycol, hover and colour MUST match either the supplied list, or if none, col1...coln."/>
   </inputs>
   <outputs>
     <data name="htmlout" format="html" label="htmlout" hidden="false"/>
@@ -94,11 +99,11 @@
     <test>
       <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/>
       <param name="input_tab" value="input_tab_sample"/>
-      <param name="xcol" value="mismatch"/>
+      <param name="xcol" value="qaccver"/>
       <param name="ycol" value="bitscore"/>
-      <param name="colourcol" value="qaccver"/>
+      <param name="colourcol" value="piden"/>
       <param name="hovercol" value="qseq"/>
-      <param name="title" value="Test title default"/>
+      <param name="title" value="Qaccver by bitscore coloured by pident. Hover shows blast match."/>
       <param name="header" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles"/>
     </test>
   </tests>
@@ -110,11 +115,13 @@
 
 .. class:: warningmark
 
+NOTE: Long strings in x and y tickmarks WILL BE TRUNCATED if they are too long - ".." is added to indicate truncation - otherwise some plots are squished.
+
 
 
-Long strings in x and y tickmarks WILL BE TRUNCATED if they are too long - ".." is added to indicate truncation - otherwise some plots are squished.
+.. class:: warningmark
 
-The evalues WILL BE CONVERTED as -log10(evalue) so they are scaled in a way that doesn't confuse plotly.express with the tiny values.
+NOTE: Blast evalues WILL BE TRANSFORMED using -log10(evalue), so they are scaled in a way that doesn't confuse plotly.express with the tiny values.
 
 
 
@@ -122,7 +129,7 @@
 
 
 
-The main reason to run this tool is to have an interactive hover text specified so it appears when hovering over each data point to supply useful information.
+The main reason to run this tool is to have an interactive hover text specified so it appears when hovering over each data point to supply useful information. 
 
 
 
@@ -150,6 +157,14 @@
 
 
 
+.. image:: pbsample.png
+
+    :height: 400
+
+    :width: 400
+
+ 
+
 ------
 
 
@@ -176,7 +191,7 @@
     args = parser.parse_args()
     df = pd.read_csv(args.input_tab, sep='\t')
     NCOLS = df.columns.size
-    MAXLEN = 40 # tricky way to truncate long axis tickmarks
+    MAXLEN = 30 # tricky way to truncate long axis tickmarks
     defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
     if len(args.header.strip()) > 0:
         newcols = args.header.split(',')
@@ -187,19 +202,22 @@
             df.columns = defaultcols
     else:
         df.columns = defaultcols
-    df['evalue'] = [-math.log(x) for x in df['evalue']] # convert so large values reflect statistical surprise
+    df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise
     if len(args.colourcol.strip()) == 0:
         fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
     else:
         fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
     if args.title:
-        ftitle=dict(text=args.title, font=dict(size=50), automargin=True)
+        ftitle=dict(text=args.title, font=dict(size=40), automargin=True)
         fig.update_layout(title=ftitle)
     for scatter in fig.data:
         scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
         scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
+        if len(args.colourcol.strip()) == 0:
+            sl = str(scatter['legendgroup'])
+            if len(sl) > MAXLEN:
+                scatter['legendgroup'] = sl[:MAXLEN]
     fig.write_html(args.htmlout)
-    fig.show()
 
 ]]></help>
   <citations>