diff seqsero.xml @ 0:6895de35a263 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqsero.xml	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">
+	<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,fastqsanger" 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.
+
+          	Below is the link to the seqsero help
+
+               https://galaxy.ravencloudhpc.com/static/toolpages/seqsero/seqsero.html
+
+        </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>