Mercurial > repos > iuc > meryl_histogram_kmers

diff histogram-kmers.xml @ 0:16b7b0d0eaea draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
author: iuc
date: Tue, 08 Oct 2024 16:43:08 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/histogram-kmers.xml	Tue Oct 08 16:43:08 2024 +0000
@@ -0,0 +1,40 @@
+<tool id="meryl_histogram_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>get k-mer frequency histogram</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    mkdir  -p ./temp_db/ &&
+    tar -xmf $input_meryldb_02 --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./temp_db/ &&
+    mv ./temp_db/* tmp.meryl &&
+    meryl histogram tmp.meryl > read-db.hist
+    ]]></command>
+    <inputs>
+        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb"/>
+    </inputs>
+    <outputs>
+        <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <output name="read_db_hist" file="output_24.read-db.hist"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool determines a k-mer frequency histogram.
+        </help>
+    <expand macro="citations"/>
+</tool>