--- a/falco.xml	Tue Sep 10 19:02:22 2024 +0000
+++ b/falco.xml	Fri Sep 27 17:41:19 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>An alternative, more performant implementation of FastQC for high throughput sequence quality control</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.2.3</token>
+        <token name="@TOOL_VERSION@">1.2.4</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <xrefs>
@@ -74,28 +74,81 @@
         </data>
     </outputs>
     <tests>
+        <!-- Test with fastq input -->
         <test expect_num_outputs="2">
             <param name="input_file" value="1000trimmed.fastq"/>
-            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_data.txt" ftype="txt"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <!-- two lines diff to allow for reported version to change -->
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
+        </test>
+        <!-- Test with fastq.gz input -->
+        <test expect_num_outputs="2">
+            <param name="input_file" value="1000trimmed.fastq.gz"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq_gz - report.+"/>
+                </assert_contents>
+            </output>
+            <!-- four lines diff to allow for reported version to change; two more to accomodate changed input file name -->
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
+        </test>
+        <!-- Test with BAM input -->
+        <test expect_num_outputs="2">
+            <param name="input_file" value="hisat_output_1.bam"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     hisat_output_1_bam - report.+"/>
+                </assert_contents>
+            </output>
+            <!-- four lines diff to allow for reported version to change; two more to accomodate changed input file name -->
+            <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/>
+        </test>
+        <!-- Test summary file option -->
+        <test expect_num_outputs="3">
+            <param name="input_file" value="1000trimmed.fastq"/>
+            <param name="generate_summary" value="true"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
+            <output name="summary_file" file="fastqc_data_summary.txt" ftype="txt"/>
         </test>
         <test expect_num_outputs="2">
             <param name="input_file" value="1000trimmed.fastq"/>
             <param name="contaminants" value="contaminant_list.txt" ftype="tabular"/>
-            <output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt" lines_diff="2"/>
         </test>
         <test expect_num_outputs="2">
             <param name="input_file" value="1000trimmed.fastq"/>
             <param name="adapters" value="adapter_list.txt" ftype="tabular"/>
-            <output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt" lines_diff="2"/>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input_file" value="1000trimmed.fastq"/>
             <param name="limits" value="limits.txt" ftype="txt"/>
-            <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/>
+            <param name="generate_summary" value="true"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="summary_file" file="fastqc_data_customlimits_summary.txt" ftype="txt"/>
         </test>
         <!-- ## The kmers param is ignored in Falco and always set to 7. If this ever gets reconsidered, this test could be uncommented.
         <test expect_num_outputs="2">
@@ -116,40 +169,49 @@
             <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/>
             <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/>
         </test> -->
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="2">
             <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
             <param name="nogroup" value="--nogroup"/>
-            <param name="generate_summary" value="true"/>
-            <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/>
-            <output name="summary_file" file="fastqc_data_nogroup_summary.txt" ftype="txt"/>
-            <assert_command>
-                <has_text text="--nogroup"/>
-            </assert_command>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt" lines_diff="2"/>
         </test>
         <test expect_num_outputs="3">
             <param name="input_file" value="1000trimmed.fastq"/>
             <param name="subsample" value="10"/>
             <param name="generate_summary" value="true"/>
-            <output name="html_file" file="fastqc_report_subsample.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_report_subsample.txt" ftype="txt"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_report_subsample.txt" ftype="txt" lines_diff="2"/>
             <output name="summary_file" file="fastqc_report_subsample_summary.txt" ftype="txt"/>
         </test>
         <test expect_num_outputs="3">
             <param name="input_file" value="1000trimmed.fastq"/>
             <param name="bisulfite" value="-bisulfite"/>
             <param name="generate_summary" value="true"/>
-            <output name="html_file" file="fastqc_report_bisulfite.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt" lines_diff="2"/>
             <output name="summary_file" file="fastqc_report_bisulfite_summary.txt" ftype="txt"/>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="2">
             <param name="input_file" value="1000trimmed.fastq"/>
             <param name="reverse_complement" value="-reverse-complement"/>
-            <param name="generate_summary" value="true"/>
-            <output name="html_file" file="fastqc_report_reverse_complement.html" ftype="html" lines_diff="2"/>
-            <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt"/>
-            <output name="summary_file" file="fastqc_report_reverse_complement_summary.txt" ftype="txt"/>
+            <output name="html_file" ftype="html">
+                <assert_contents>
+                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                </assert_contents>
+            </output>
+            <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt" lines_diff="2"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -159,15 +221,15 @@
 
 💚️ With its superior performance Falco saves computational resources and gives you back results faster than FastQC.
 
-We recommend it for most use cases (but see below for exceptions). 💚️
+We recommend it for most use cases (but see below for rare exceptions). 💚️
 
 The main functions of Falco are very similar to those of FastQC:
 
 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
 - Providing a quick overview to tell you in which areas there may be problems
 - Summary graphs and tables to quickly assess your data
-- Export of results to an HTML based permanent report
-- Offline operation to allow automated generation of reports without running the interactive application
+- Export of results to an HTML-based report
+
 
 .. class:: infomark
 
@@ -181,13 +243,10 @@
 
   Falco doesn't currently support fastq.bz2 as input format meaning Galaxy has to perform a relatively slow format conversion before running the tool, which together makes the analysis slower than with FastQC.
 
-- you are interested in PolyA and PolyG statistics in the Adapter Content section of the quality report
-
-  Falco doesn't currently calculate statistics for these "Adapters" by default.
+- you need the HTML report to be viewable offline
 
-- your input consists of *mapped* reads in SAM/BAM format
-
-  Due to a bug in the current version of Falco, reads mapped to the reverse strand of the reference genome are not handled correctly and reported metrics are wrong!
+  The current version of Falco relies on plotly to generate the graphs in the HTML report dynamically each time it's viewed.
+  MultiQC plots generated from Falco's raw data output are, of course, viewable offline just like the ones generated from FastQC output.
 
 -----