--- a/falco.xml	Sun Jun 30 11:28:11 2024 +0000
+++ b/falco.xml	Tue Sep 10 19:02:22 2024 +0000
@@ -1,10 +1,14 @@
-<tool id="falco" name="Falco" version="1.2.2+galaxy1" profile="21.05">
+<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="@VERSION_SUFFIX@">0</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">falco</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="1.2.2">falco</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">falco</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
@@ -60,7 +64,7 @@
         <param argument="-subsample" type="integer" value="1" min="1" label="Subsampling Factor" help="This makes falco faster (but possibly less accurate) by only processing reads that are multiple of this value (using 0-based indexing to number reads)"/>
         <param argument="-bisulfite" type="boolean" truevalue="-bisulfite" falsevalue="" checked="False" label="Bisulfite Sequencing" help="This parameter indicates whether the reads are from whole genome bisulfite sequencing. When enabled, Falco will account for the expected increase in Ts and decrease in Cs in the base content."/>
         <param argument="reverse_complement" type="boolean" truevalue="-reverse-complement" falsevalue="" checked="False" label="Reverse Complement" help="This parameter specifies whether the input sequences are reverse-complemented. When enabled, all modules in Falco will be tested by swapping A/T and C/G."/>
-        <param name="generate_summary" type="boolean" truevalue="" falsevalue="-skip-summary" checked="False" label="Generate summary output of QC test results" />
+        <param name="generate_summary" type="boolean" truevalue="" falsevalue="-skip-summary" checked="False" label="Generate summary output of QC test results"/>
     </inputs>
     <outputs>
         <data format="html" name="html_file" from_work_dir="fastqc_report.html" label="${tool.name} on ${on_string}: Webpage"/>
@@ -93,7 +97,6 @@
             <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"/>
         </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">
             <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
@@ -113,7 +116,6 @@
             <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">
             <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
             <param name="nogroup" value="--nogroup"/>