falco - Update to version 1.3.0 (#7945)

* falco - Update to version 1.3.0, update profile to 25.0, remove .lint_skip, and update tests and test files

* Add profile token

Author: RZ9082

tools/falco/.lint_skip

@@ -1,8 +1,9 @@
-<tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>An alternative, more performant implementation of FastQC for high throughput sequence quality control</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.2.4</token>
+        <token name="@TOOL_VERSION@">1.3.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">25.0</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">falco</xref>
@@ -79,7 +80,7 @@
             <param name="input_file" value="1000trimmed.fastq"/>
             <output name="html_file" ftype="html">
                 <assert_contents>
-                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <!-- two lines diff to allow for reported version to change -->
@@ -90,7 +91,7 @@
             <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.+"/>
+                  <has_line_matching expression="\s*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 -->
@@ -101,7 +102,7 @@
             <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.+"/>
+                  <has_line_matching expression="\s*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 -->
@@ -113,7 +114,7 @@
             <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.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
@@ -124,7 +125,7 @@
             <param name="contaminants" value="contaminant_list.txt" ftype="tabular"/>
             <output name="html_file" ftype="html">
                 <assert_contents>
-                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt" lines_diff="2"/>
@@ -134,7 +135,7 @@
             <param name="adapters" value="adapter_list.txt" ftype="tabular"/>
             <output name="html_file" ftype="html">
                 <assert_contents>
-                  <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt;     1000trimmed_fastq - report.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt" lines_diff="2"/>
@@ -145,7 +146,7 @@
             <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.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <output name="summary_file" file="fastqc_data_customlimits_summary.txt" ftype="txt"/>
@@ -171,10 +172,10 @@
         </test> -->
         <test expect_num_outputs="2">
             <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
-            <param name="nogroup" value="--nogroup"/>
+            <param name="nogroup" 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.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt" lines_diff="2"/>
@@ -185,30 +186,30 @@
             <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.+"/>
+                  <has_line_matching expression="\s*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="bisulfite" value="true"/>
             <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.+"/>
+                  <has_line_matching expression="\s*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="2">
             <param name="input_file" value="1000trimmed.fastq"/>
-            <param name="reverse_complement" value="-reverse-complement"/>
+            <param name="reverse_complement" 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.+"/>
+                  <has_line_matching expression="\s*1000trimmed_fastq - report"/>
                 </assert_contents>
             </output>
             <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt" lines_diff="2"/>