diff split.xml @ 0:bffcba7ce9b5 draft

planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split.xml	Fri Apr 05 10:29:17 2024 +0000
@@ -0,0 +1,38 @@
+<tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+    <description>Split a pairsam file into pairs and SAM/BAM</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        pairtools split
+            '$pairsam_path'
+            --output-pairs '$output_pairs'
+            --output-sam ./output.bam
+            --nproc-in \${GALAXY_SLOTS:-4}
+            --nproc-out \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/>
+    </inputs>
+    <outputs>
+        <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" />
+        <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" />
+    </outputs>
+    <tests>
+        <!--Test default parameters-->
+        <test expect_num_outputs="2">
+            <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/>
+            <output name="output_pairs" ftype="4dn_pairs" file="output_pairs_split.pairs" lines_diff="10"/>
+            <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **Pairtools split**
+
+        Restore a SAM/BAM file from SAM1 and SAM2 fields of a `pairsam` file. Create a `pairs` file without SAM1/SAM2 fields.
+              
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>