Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads

diff adjust_bracken_kreport_for_unclassified_reads.xml @ 3:899a650587ed draft default tip

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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
author public-health-bioinformatics
date Thu, 27 Oct 2022 19:13:25 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/adjust_bracken_kreport_for_unclassified_reads.xml	Thu Oct 27 19:13:25 2022 +0000
@@ -0,0 +1,29 @@
+<tool id="adjust_bracken_kreport_for_unclassified_reads" name="Adjust Kraken-Style Bracken Report for Unclassified Reads" version="0.1.0+galaxy0">
+    <description>Adjust kraken-style bracken report to account for unclassified reads</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        '$__tool_directory__/adjust_bracken_kreport_for_unclassified_reads.py'
+        --kraken-report '${kraken_report}'
+        --kraken-style-bracken-report '${kraken_style_bracken_report}'
+        > ${adjusted_report}
+    ]]></command>
+    <inputs>
+        <param name="kraken_report" type="data" format="txt" />
+        <param name="kraken_style_bracken_report" type="data" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="adjusted_report" label="Adjusted Report" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="kraken_report" value="input/SRR17619849_kraken2.txt"/>
+            <param name="kraken_style_bracken_report" value=""/>
+            <output name="adjusted_report" file="" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>