--- a/stringtie_merge.xml	Mon Jan 30 12:01:28 2023 +0000
+++ b/stringtie_merge.xml	Tue Apr 30 11:53:08 2024 +0000
@@ -1,11 +1,11 @@
 <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
@@ -26,35 +26,35 @@
         -o '$out_gtf' '$inputs'
     ]]></command>
     <inputs>
-        <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
-        <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
-        <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" />
-        <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" />
-        <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" />
-        <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" />
-        <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
-        <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" />
-        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
+        <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format"/>
+        <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging"/>
+        <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge"/>
+        <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge"/>
+        <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge"/>
+        <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge"/>
+        <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction"/>
+        <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together"/>
+        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them"/>
     </inputs>
     <outputs>
-        <data name="out_gtf" format="gtf" />
+        <data name="out_gtf" format="gtf"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
-            <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf"/>
+            <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf"/>
+            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <test>
-            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
             <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <test>
-            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
             <output name="out_gtf" ftype="gtf">
                 <assert_contents>
-                    <has_text text="stringtie --merge" />
+                    <has_text text="stringtie --merge"/>
                 </assert_contents>
             </output>
         </test>