Mercurial > repos > charles_s_test > seqsero2

diff seqsero.xml.precitation @ 0:6895de35a263 draft

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planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
author charles_s_test
date Thu, 19 Oct 2017 18:16:51 -0400
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+++ b/seqsero.xml.precitation	Thu Oct 19 18:16:51 2017 -0400
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+<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
+        <requirement type="package" version="1.69">biopython</requirement>
+        <requirement type="package" >samtools</requirement>
+        <description>Salmonella Serotype Prediction from Paired-End Reads</description>
+        <command interpreter="python2.7">
+                run_seqsero_batch_galaxy.py $input1 <!--$input2-->
+                <!--test_bioblend.py $input1 $input2-->
+        </command>
+        <inputs>
+                <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
+                <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
+        </inputs>
+        <outputs>
+                <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
+                <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
+        </outputs>
+        <help>
+                This tool predicts Salmonella serotypes from shotgun WGS data.
+		<description
+			xlink:type="simple"
+			xlink:href="/nfs/sw/apps/galaxy/static/toolpages/seqsero/seqsero.html"
+			xlink:show="SeqSero documentation"
+		</description>
+        </help>
+	<citations>
+		<citation type="bibtex"> 
+		@Article{pmid25762776,
+		  	Author="Zhang, S.  and Yin, Y.  and Jones, M. B.  and Zhang, Z.  and Deatherage Kaiser, B. L.  and Dinsmore, B. A.  and Fitzgerald, C.  and Fields, P. I.  and Deng, X. ",
+   			Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
+   			Journal="J. Clin. Microbiol.",
+   			Year="2015",
+   			Volume="53",
+   			Number="5",
+   			Pages="1685--1692",
+   			Month="May"
+		}
+		</citation>
+	</citations>
+        <stdio>
+                <exit_code range="0:" level="warning"/>
+                <regex match="Error:"/>
+        </stdio>
+</tool>
+