# HG changeset patch
# User galaxyp
# Date 1536962657 14400
# Node ID 00c4b28150bd438a8706e58077583925095f7563

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d

diff -r 000000000000 -r 00c4b28150bd test-data/fake_input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fake_input.txt	Fri Sep 14 18:04:17 2018 -0400
@@ -0,0 +1,1 @@
+This is a fake input, I was not able to find a very small RAW file.
diff -r 000000000000 -r 00c4b28150bd thermo_converter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/thermo_converter.xml	Fri Sep 14 18:04:17 2018 -0400
@@ -0,0 +1,56 @@
+<tool id="thermo_raw_file_converter" name="Thermo" version="0.0.1">
+    <description>RAW file converter (beta)</description>
+    <requirements>
+        <requirement type="package" version="0.0.2018.09.07">ThermoRawFileParser</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+
+ln -s '$input' ./input.raw &&
+
+ThermoRawFileParser.sh
+    -i=input.raw
+    -o=./
+    -f=1
+    #if $metadata:
+        --metadata=1
+    #end if
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" />
+        <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False"
+            label="Output metadata" help="" />
+    </inputs>
+    <outputs>
+        <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}" />
+        <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata">
+            <filter>metadata</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fake_input.txt"/>
+            <assert_command>
+                <has_text text="ThermoRawFileParser.sh"/>
+            </assert_command>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project.
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">@misc{Galaxy Proteomics Tools,
+        author = {Niels Hulstaert, et al.},
+        title = {Galaxy Proteomics Tools},
+        publisher = {GitHub},
+        journal = {GitHub repository},
+        year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}}
+        </citation>
+    </citations>
+</tool>
+