--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/centrifuge_process.xml	Wed Jun 22 16:13:46 2022 -0400
@@ -0,0 +1,55 @@
+<tool id="centrifuge_process" name="Take in centrifuge output, report, FASTQ and extract sequence IDs belonging to user supplied taxa name of interest." version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="3.9">python</requirement>
+        <requirement type="package">biopython</requirement>
+        <requirement type="package">pandas</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t '$output1'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="txt" />
+	<param type="data" name="input2" format="txt" />
+	<param type="text" name="input3" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="FAL11127.centrifuge.output.txt"/>
+	    <param name="input2" value="FAL11127.centrifuge.report.txt"/>
+	    <param name="input3" value="Escherichia coli"/>
+            <output name="output1" file="FAL11127.process-centrifuge-bug-ids.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+usage: process_centrifuge_output.py [-h] [-v] [-i INPUT_FASTQ] -t TAXA_FILTERED_FASTQ_FILE -r CENT_REPORT -o
+                                    CENT_OUTPUT -b BUG
+
+This script is part of the centriflaken pipeline: It processes centrifuge output and produces either a filtered FASTQ
+or a text file of FASTQ IDs based on the supplied taxa/bug
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -v                    For more verbose output
+  -i INPUT_FASTQ        Path to input FASTQ file (same as input to centrifuge). If not mentioned, a text file of
+                        sequence IDs are produced instead of a FASTQ file
+  -t TAXA_FILTERED_FASTQ_FILE
+                        Path to output FASTQ or output text file filtered by the taxa specified
+  -r CENT_REPORT        Path to centrifuge report
+  -o CENT_OUTPUT        Path to centrifuge output
+  -b BUG                Name or fragment of name of the bug by which reads are extracted
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{gitlabcpipescentriflaken,
+  author = {Konganti, Kranti},
+  year = {2022},
+  title = {CPIPES},
+  publisher = {GitLab},
+  journal = {GitLab repository},
+  url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes},
+}</citation>
+    </citations>	
+</tool>