diff isa2mzml.xml @ 0:975585306dc4 draft default tip

"planemo upload commit c2694fb4aa55c4f25eb53db73496eaf5e56d7872"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isa2mzml.xml	Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,77 @@
+<!-- vi: se fdm=marker : -->
+<tool id="isa2mzml" name="ISA to mzML" version="1.3.0">
+
+	<description>Extract mzML files from an ISA dataset and output a collection of mzML dataset.</description>
+
+	<!-- Command {{{1 -->
+
+	<command><![CDATA[
+		## @@@BEGIN_CHEETAH@@@
+
+		$__tool_directory__/extract-from-isa
+		-i "$isa.extra_files_path"
+		-e mzML
+		-o mzML
+
+		## @@@END_CHEETAH@@@
+	]]></command>
+
+	<!-- Inputs {{{1 -->
+
+	<inputs>
+		<param name="isa" label="ISA" type="data" format="isa-tab"/>
+	</inputs>
+
+	<!-- Outputs {{{1 -->
+
+    <outputs>
+		<collection name="mzML" type="list" label="mzML files">
+			<discover_datasets pattern="(?P&lt;designation&gt;.+)\.[mM][zZ][mM][lL]$" directory="mzML" format="mzml"/>
+		</collection>
+	</outputs>
+
+	<!-- Tests {{{1 -->
+	<tests>
+		<test>
+			<param name="isa" value="mzml_study.zip" ftype="isa-tab"/>
+			<output_collection name="mzML" type="list" count="1">
+				<element name="empty" file="mzml_study_output/empty.mzML" ftype="mzml"/>
+			</output_collection>
+		</test>
+	</tests>
+
+	<!-- Help {{{1 -->
+    <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to mzML
+====================
+
+Extract mzML files contained inside an ISA archive.
+
+-----
+Input
+-----
+
+ISA dataset
+===========
+
+The ISA-Tab dataset from which to extract the files.
+
+------
+Output
+------
+
+The output is a collection of mzML files.
+
+<!-- @@@END_RST@@@ -->
+    </help>
+
+	<!-- Citations {{{1 -->
+    <citations>
+        <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
+        <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
+    </citations>
+
+</tool>