Mercurial > repos > recetox > recetox_xmsannotator_simple

changeset 1:fa85bd6fd713 draft

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"planemo upload commit e434c430917b52ef21b96f0231663c1f1dda34f9-dirty"
author recetox
date Thu, 17 Sep 2020 08:39:26 +0000
parents 4cf6d71da794
children c72233720bdc
files recetox_xmsannotator_macros.xml recetox_xmsannotator_simple.xml
diffstat 2 files changed, 11 insertions(+), 8 deletions(-) [+]
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line diff
--- a/recetox_xmsannotator_macros.xml	Tue Aug 25 11:45:18 2020 +0000
+++ b/recetox_xmsannotator_macros.xml	Thu Sep 17 08:39:26 2020 +0000
@@ -2,7 +2,7 @@
     <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>
+            <container type="docker">registry.gitlab.ics.muni.cz:443/recetox/mass-spectrometry/xmsannotator:v2.0</container>
         </requirements>
     </xml>
 
--- a/recetox_xmsannotator_simple.xml	Tue Aug 25 11:45:18 2020 +0000
+++ b/recetox_xmsannotator_simple.xml	Thu Sep 17 08:39:26 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="deployment">
+<tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="v2.0">
     <macros>
         <import>recetox_xmsannotator_macros.xml</import>
     </macros>
@@ -7,21 +7,24 @@
 
     <command detect_errors="aggressive"><![CDATA[
         Rscript -e 'annotation <- xmsannotator::simple_annotation(
-                        data = arrow::read_feather("$peaks"),
+                        peaks = arrow::read_feather("$peaks"),
+                        adducts = rhdf5::h5read("$adducts", "adducts"),
                         metabolites = rhdf5::h5read("$metabolites", "metabolites"),
-                        mz_tolerance_ppm = as.double($mz_tolerance)
+                        mz_tolerance = as.double($mass_tolerance)
                    )'
                 -e 'arrow::write_feather(annotation, "$annotation")'
     ]]></command>
 
     <inputs>
-        <expand macro="peaks"/>
-        <expand macro="metabolites"/>
-        <expand macro="mz_tolerance"/>
+        <param name="peaks" type="data" format="feather" label="Peaks" help="Table of peak intensities."/>
+        <param name="metabolites" type="data" format="h5" label="Metabolite database"/>
+        <param name="adducts" type="data" format="h5" label="Adduct database"/>
+
+        <param name="mass_tolerance" type="float" value="10" min="0" label="Mass tolerance [ppm]" help="Mass tolerance in ppm for database matching."/>
     </inputs>
 
     <outputs>
-        <expand macro="annotation_output"/>
+        <data format="feather" name="annotation"/>
     </outputs>
 
     <help><![CDATA[]]></help>