diff nugen_nudup.xml @ 4:0d24a02c555f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit 26045b518c15c3f18996f6dc2af7064a9c1941dd

--- a/nugen_nudup.xml	Mon Feb 05 14:40:52 2018 -0500
+++ b/nugen_nudup.xml	Fri Mar 15 12:40:38 2024 +0000
@@ -2,6 +2,9 @@
     <description>
         mark/remove PCR duplicates based on molecular tags
     </description>
+    <xrefs>
+        <xref type="bio.tools">nudup</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="2.3.3">nudup</requirement>
     </requirements>
@@ -38,10 +41,8 @@
             format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ
             file containing the molecular tag sequence for each read name in
             the corresponding SAM/BAM file" />
-        <param type="boolean" argument="--paired-end"
-            label="Paired-end deduping" name="paired_end"
-            truevalue="--paired-end" falsevalue=""
-            checked="false"
+        <param type="boolean" argument="--paired-end" label="Paired-end deduping"
+            truevalue="--paired-end" falsevalue="" checked="false"
             help="use paired end deduping with template. SAM/BAM alignment
             must contain paired end reads. Degenerate read pairs
             (alignments for one read of pair) will be discarded." />
@@ -51,7 +52,7 @@
             counts in from the 3' END of the read." />
         <param type="integer" argument="--length" label="Tag sequence length"
             value="6" help="length of molecular tag sequence" />
-        <param type="boolean" argument="--rmdup-only" name="rmdup_only"
+        <param type="boolean" argument="--rmdup-only"
             label="Only output BAM with duplicates removed"
             truevalue="--rmdup-only" falsevalue="" checked="false"
             help="Do not ouput BAM with duplicates marked. Default is to ouput
@@ -71,7 +72,7 @@
               from_work_dir="prefix_dup_log.txt" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="nudup_test_1.bam" ftype="bam" />
             <param name="umi_fastq" value="nudup_umis.fastq"
                 ftype="fastqsanger" />
@@ -81,7 +82,7 @@
             <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
             <output name="log" file="nudup_log_1.txt" ftype="txt" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="nudup_test_1.bam" ftype="bam" />
             <param name="umi_fastq" value="nudup_umis.fastq.gz"
                 ftype="fastqsanger.gz" />