diff seqsero.xml.2b @ 8:b04931a9fe71 draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqsero.xml.2b	Tue Nov 28 18:55:00 2017 -0500
@@ -0,0 +1,41 @@
+<bookstore xmlns:xlink="http://www.w3.org/1999/xlink">
+
+<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.-->
+               .._htmlFile: "/nfs/sw/apps/galaxy/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>