diff samtools_ampliconclip.xml @ 2:6a8febad1f6c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit cd62639660bef041ba14ecff337fb98e84e75d8a

--- a/samtools_ampliconclip.xml	Mon Aug 15 09:15:14 2022 +0000
+++ b/samtools_ampliconclip.xml	Mon Nov 20 22:14:18 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>clip primer bases from bam files</description>
     <macros>
         <import>macros.xml</import>
@@ -29,11 +29,11 @@
         <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
         <param name="input_bam" type="data" format="bam" label="BAM file" />
         <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
-        <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
-        <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
-        <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
+        <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
+        <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
+        <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
         <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
-        <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
+        <param argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
     
     </inputs>
     <outputs>