Mercurial > repos > iuc > samblaster

changeset 1:cf4ad98037d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
author iuc
date Sat, 05 Oct 2024 13:29:37 +0000
parents aa72470e14f7
children 037e8ed9d3c9
files samblaster.xml
diffstat 1 files changed, 17 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/samblaster.xml	Mon Dec 19 15:18:40 2016 -0500
+++ b/samblaster.xml	Sat Oct 05 13:29:37 2024 +0000
@@ -1,7 +1,14 @@
-<tool id="samblaster" name="samblaster" version="0.1.24">
+<tool id="samblaster" name="samblaster" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
     <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.24</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">samblaster</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package" version="0.1.24">samblaster</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">samblaster</requirement>
         <requirement type="package" version="0.6.5">sambamba</requirement>
     </requirements>
     <version_command>samblaster --version</version_command>
@@ -55,24 +62,24 @@
         <param argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/>
     </inputs>
     <outputs>
-        <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam">
+        <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: alignments" from_work_dir="output.bam">
             <filter>output</filter>
         </data>
-        <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam">
+        <data name="discordant_bam" format="bam" label="${tool.name} on ${on_string}discordant alignments" from_work_dir="discordant.bam">
             <filter>discordantFile</filter>
         </data>
-        <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam">
+        <data name="splitter_bam" format="bam" label="${tool.name} on ${on_string}: split alignments" from_work_dir="splitter.bam">
             <filter>splitterFile</filter>
         </data>
-        <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq">
+        <data name="unmapped_fastq" format="fastqsanger" label="${tool.name} on ${on_string}: unmapped fastq" from_work_dir="unmapped.fastq">
             <filter>unmappedFile</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="sr.input.bam"/>
             <param name="output" value="true"/>
-            <param name="discordandFile" value="false"/>
+            <param name="discordantFile" value="false"/>
             <param name="splitterFile" value="true"/>
             <param name="unmappedFile" value="true"/>
             <output name="output_bam" file="output.bam" compare="sim_size"/>
@@ -83,10 +90,10 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="sr.input.sam.gz" ftype="sam"/>
             <param name="output" value="true"/>
-            <param name="discordandFile" value="false"/>
+            <param name="discordantFile" value="false"/>
             <param name="splitterFile" value="true"/>
             <param name="unmappedFile" value="true"/>
             <output name="output_bam" file="output.bam" compare="sim_size"/>