Mercurial > repos > kkonganti > centrifuge_process

comparison centrifuge_process.xml @ 1:48eebe68ec69

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"planemo upload"
author kkonganti
date Wed, 22 Jun 2022 16:56:23 -0400
parents 00fa638e833e
children 5860f4569cda
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0:00fa638e833e 1:48eebe68ec69
3 <requirement type="package" version="3.9">python</requirement> 3 <requirement type="package" version="3.9">python</requirement>
4 <requirement type="package">biopython</requirement> 4 <requirement type="package">biopython</requirement>
5 <requirement type="package">pandas</requirement> 5 <requirement type="package">pandas</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t '$output1' 8 $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t FAL11127.process-centrifuge-bug-ids.txt
9 ]]></command> 9 ]]></command>
10 <inputs> 10 <inputs>
11 <param type="data" name="input1" format="txt" /> 11 <param type="data" name="input1" format="txt" />
12 <param type="data" name="input2" format="txt" /> 12 <param type="data" name="input2" format="txt" />
13 <param type="text" name="input3" format="txt" /> 13 <param type="text" name="input3" format="txt" />
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
16 <data name="output1" format="txt" /> 16 <data name="output" format="txt" from_work_dir="FAL11127.process-centrifuge-bug-ids.txt" />
17 </outputs> 17 </outputs>
18 <tests> 18 <tests>
19 <test> 19 <test>
20 <param name="input1" value="FAL11127.centrifuge.output.txt"/> 20 <param name="input1" value="FAL11127.centrifuge.output.txt"/>
21 <param name="input2" value="FAL11127.centrifuge.report.txt"/> 21 <param name="input2" value="FAL11127.centrifuge.report.txt"/>
22 <param name="input3" value="Escherichia coli"/> 22 <param name="input3" value="Escherichia coli"/>
23 <output name="output1" file="FAL11127.process-centrifuge-bug-ids.txt"/> 23 <output name="output" file="FAL11127.process-centrifuge-bug-ids.txt"/>
24 </test> 24 </test>
25 </tests> 25 </tests>
26 <help><![CDATA[ 26 <help><![CDATA[
27 usage: process_centrifuge_output.py [-h] [-v] [-i INPUT_FASTQ] -t TAXA_FILTERED_FASTQ_FILE -r CENT_REPORT -o 27 usage: process_centrifuge_output.py [-h] [-v] [-i INPUT_FASTQ] -t TAXA_FILTERED_FASTQ_FILE -r CENT_REPORT -o
28 CENT_OUTPUT -b BUG 28 CENT_OUTPUT -b BUG