# HG changeset patch
# User jpayne
# Date 1561657602 14400
# Node ID 00c8dbe0549aa53b5437bbc5886800c958484dc3

planemo upload

diff -r 000000000000 -r 00c8dbe0549a shigatyper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shigatyper.xml	Thu Jun 27 13:46:42 2019 -0400
@@ -0,0 +1,43 @@
+<tool id="shigatyper" name="ShigaTyper" version="1.0.5">
+    <description>Shigella genoserotyping</description>
+    <requirements>
+        <requirement type="package" version="1.0.5">shigatyper</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" />
+        <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" />
+    </inputs>
+    <outputs>
+        <data name="output1" label="Shigella serotype prediction" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
+            <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
+            <output name="output1" file="output.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
+
+positional arguments:
+  read1
+  read2
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubshigatyper,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {shigatyper},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CFSAN-Biostatistics/shigatyper},
+}</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 00c8dbe0549a test-data/CFSAN029786_S10_L001_R1_001.fastq.gz
Binary file test-data/CFSAN029786_S10_L001_R1_001.fastq.gz has changed
diff -r 000000000000 -r 00c8dbe0549a test-data/CFSAN029786_S10_L001_R2_001.fastq.gz
Binary file test-data/CFSAN029786_S10_L001_R2_001.fastq.gz has changed
diff -r 000000000000 -r 00c8dbe0549a test-data/output.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular	Thu Jun 27 13:46:42 2019 -0400
@@ -0,0 +1,2 @@
+sample	prediction	ipaB
+CFSAN029786	Shigella dysenteriae serotype 3	+