Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads

diff adjust_bracken_for_unclassified_reads.xml @ 0:3ab9d37e547e draft

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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 0d1d1f356cdfd8ef6dbcdd1bfe76c4637587ff53"
author public-health-bioinformatics
date Thu, 10 Mar 2022 21:35:14 +0000
parents
children 3cde438eb222
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/adjust_bracken_for_unclassified_reads.xml	Thu Mar 10 21:35:14 2022 +0000
@@ -0,0 +1,34 @@
+<tool id="adjust_bracken_for_unclassified_reads" name="Adjust Bracken Report for Unclassified Reads" version="0.1.0">
+    <description>Adjust bracken report to account for unclassified reads</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        '$__tool_directory__/adjust_bracken_for_unclassified_reads.py'
+        --kraken-report '${kraken_report}'
+        --bracken-abundances '${bracken_abundances}'
+        > ${adjusted_bracken_report}
+    ]]></command>
+    <inputs>
+        <param name="kraken_report" type="data" format="txt" />
+        <param name="bracken_abundances" type="data" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="adjusted_bracken_report" label="Adjusted Report" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="kraken_report" value="input/SRR17619849_kraken2.txt"/>
+            <param name="bracken_abundances" value="input/SRR17619849_bracken_abundances.tsv"/>
+            <output name="adjusted_bracken_report" file="output/SRR17619849_bracken_abundances_adjusted.tsv" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="kraken_report" value="input/SRR17907745_kraken2.txt"/>
+            <param name="bracken_abundances" value="input/SRR17907745_bracken_abundances.tsv"/>
+            <output name="adjusted_bracken_report" file="output/SRR17907745_bracken_abundances_adjusted.tsv" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>