--- a/stringtie.xml	Mon Oct 31 20:08:02 2022 +0000
+++ b/stringtie.xml	Mon Jan 30 12:01:28 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>transcript assembly and quantification</description>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>
@@ -221,13 +221,13 @@
                     <valid initial="string.letters,string.digits"></valid>
                 </sanitizer>
             </param>
-            <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.15" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.15"/>
+            <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.05"/>
             <param name="min_tlen" argument="-m" type="integer" min="0" value="200" label="Minimum assembled transcript length" help="Sets the minimum length allowed for the predicted transcripts. Default: 200"/>
             <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10" />
             <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1" />
-            <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
+            <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="1" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
             <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/>
-            <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads"  help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
+            <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="1" label="Fraction of bundle allowed to be covered by multi-hit reads"  help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
             <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />
             <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
             <param name="point_features" type="data" format="tabular" optional="true" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/>
@@ -408,7 +408,7 @@
             <param name="use_guide" value="yes" />
             <param name="guide_gff_select" value="cached" />
             <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf"  compare="re_match" sort="true"/>
+            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!-- Test mixed reads input -->
         <test expect_num_outputs="1">
@@ -417,7 +417,13 @@
                 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
             </conditional>            
-            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="output_gtf" ftype="gtf">
+                <assert_contents>
+                    <has_text text="5.043160"/>
+                    <has_text text="StringTie version @TOOL_VERSION@"/>
+                    <has_n_lines n="87"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test cram input -->
         <test expect_num_outputs="1">
@@ -429,7 +435,7 @@
             <output name="output_gtf" ftype="gtf">
                 <assert_contents>
                     <has_text text="gi|251831106|ref|NC_012920.1|"/>
-                    <has_text text="StringTie version 2.2.1"/>
+                    <has_text text="StringTie version @TOOL_VERSION@"/>
                 </assert_contents>
             </output>
         </test>