# HG changeset patch
# User iuc
# Date 1638270094 0
# Node ID 333a6e13b62234b8be3755501ea0e3f2b49cc346
# Parent  258d696dbd7ed0f5c5da6203b406d2a163d42cf6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938"

diff -r 258d696dbd7e -r 333a6e13b622 macros.xml
--- a/macros.xml	Sat Sep 25 18:20:22 2021 +0000
+++ b/macros.xml	Tue Nov 30 11:01:34 2021 +0000
@@ -1,9 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">2.1.7</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement>
-        <requirement type="package" version="1.13">samtools</requirement>
+        <requirement type="package" version="1.14">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
diff -r 258d696dbd7e -r 333a6e13b622 stringtie.xml
--- a/stringtie.xml	Sat Sep 25 18:20:22 2021 +0000
+++ b/stringtie.xml	Tue Nov 30 11:01:34 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@">
+<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>transcript assembly and quantification</description>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>
@@ -78,6 +78,9 @@
 -M '$adv.bundle_fraction'
 $adv.disable_trimming
 $adv.multi_mapping
+#if $adv.point_features
+    --ptf $adv.point_features
+#end if
 #if $adv.abundance_estimation:
     -A '$gene_abundance_estimation'
 #end if
@@ -226,7 +229,7 @@
             <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="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)."/>
+            <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)."/>
         </section>
     </inputs>
     <outputs>
diff -r 258d696dbd7e -r 333a6e13b622 stringtie_merge.xml
--- a/stringtie_merge.xml	Sat Sep 25 18:20:22 2021 +0000
+++ b/stringtie_merge.xml	Tue Nov 30 11:01:34 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@">
+<tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>transcripts</description>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>