# HG changeset patch
# User recetox
# Date 1598355918 0
# Node ID 4cf6d71da794802c095161e475842a22cfd5b048

"planemo upload commit 5d3c80fb59c7d68a3d4ae26119821bc8d6fd65f2-dirty"

diff -r 000000000000 -r 4cf6d71da794 recetox_xmsannotator_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_xmsannotator_macros.xml	Tue Aug 25 11:45:18 2020 +0000
@@ -0,0 +1,36 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package">recetox_datatypes</requirement>
+            <container type="docker">registry.gitlab.ics.muni.cz:443/recetox/mass-spectrometry/xmsannotator:deployment</container>
+        </requirements>
+    </xml>
+
+    <xml name="peaks">
+        <param name="peaks" type="data" format="peak_table.feather" label="Peak intensity table"/>
+    </xml>
+
+    <xml name="metabolites">
+        <!-- <param name="metabolites" type="select" label="Metabolite database">
+            <options from_data_table="recetox_metabolite_databases">
+                <column name="name" index="2"/>
+                <column name="value" index="3"/>
+            </options>
+        </param> -->
+        <param name="metabolites" type="data" format="metabolites.h5" label="Metabolite database"/>
+    </xml>
+
+    <xml name="mz_tolerance">
+        <param name="mz_tolerance" type="float" value="10" min="0" label="Mass tolerance [ppm]" help="Mass tolerance in ppm for database matching."/>
+    </xml>
+
+    <xml name="annotation_output">
+        <data format="annotated_peak_list.feather" name="annotation"/>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1021/acs.analchem.6b01214</citation>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r 4cf6d71da794 recetox_xmsannotator_simple.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recetox_xmsannotator_simple.xml	Tue Aug 25 11:45:18 2020 +0000
@@ -0,0 +1,29 @@
+<tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="deployment">
+    <macros>
+        <import>recetox_xmsannotator_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript -e 'annotation <- xmsannotator::simple_annotation(
+                        data = arrow::read_feather("$peaks"),
+                        metabolites = rhdf5::h5read("$metabolites", "metabolites"),
+                        mz_tolerance_ppm = as.double($mz_tolerance)
+                   )'
+                -e 'arrow::write_feather(annotation, "$annotation")'
+    ]]></command>
+
+    <inputs>
+        <expand macro="peaks"/>
+        <expand macro="metabolites"/>
+        <expand macro="mz_tolerance"/>
+    </inputs>
+
+    <outputs>
+        <expand macro="annotation_output"/>
+    </outputs>
+
+    <help><![CDATA[]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 4cf6d71da794 tool-data/recetox_metabolite_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/recetox_metabolite_databases.loc.sample	Tue Aug 25 11:45:18 2020 +0000
@@ -0,0 +1,5 @@
+# This file has the format (white space characters are
+# TAB characters):
+#
+# <value>	<name>	<date>	<path>
+#
\ No newline at end of file
diff -r 000000000000 -r 4cf6d71da794 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Aug 25 11:45:18 2020 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="recetox_metabolite_databases" comment_char="#">
+        <columns>value, date, name, path</columns>
+        <file path="tool-data/recetox_metabolite_databases.loc" />
+    </table>
+</tables>
\ No newline at end of file