diff filterFragSpectra.xml @ 14:a9928d2ecde6 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc

--- a/filterFragSpectra.xml	Fri Sep 27 09:31:42 2019 -0400
+++ b/filterFragSpectra.xml	Wed Nov 27 12:39:38 2019 +0000
@@ -5,17 +5,13 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command interpreter="Rscript"><![CDATA[
+    <expand macro="requirements" />
+    <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[
         filterFragSpectra.R
-            --out_rdata=$filterFragSpectra_output_rdata
-            --out_peaklist_prec=$filterFragSpectra_output_prec_tsv
-            --out_peaklist_frag=$filterFragSpectra_output_frag_tsv
-            --pa="$pa"
+            --out_rdata='$filterFragSpectra_output_rdata'
+            --out_peaklist_prec='$filterFragSpectra_output_prec_tsv'
+            --out_peaklist_frag='$filterFragSpectra_output_frag_tsv'
+            --pa='$pa'
             --ilim=$ilim
             --plim=$plim
             --ra=$ra
@@ -24,43 +20,43 @@
             $rmp
     ]]></command>
     <inputs>
-        <param name="pa" type="data" 
+        <param argument="--pa" type="data"
                label="purityA object with fragmentation linked to XCMS features" format="rdata"
                help="purityA object saved as 'pa' in a RData file where fragmentation has
                      been linked to XCMS features(output from frag4feature tool)"/>
-        <param name="plim" type="float" value="0.5" help=""
+        <param argument="--plim" type="float" value="0.5" help=""
                label="Miniumum precursor ion purity of the associated precursor for
                      fragmentation spectra scan"  />
-        <param name="ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
-        <param name="ra" type="float" min="0.0" max="1.0" value="0.0" 
+        <param argument="--ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
+        <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0"
                label="Relative abundance threshold" help="" />
-        <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
-        <param name="snmeth" type="select" label="Function to calculate noise." help="" >
+        <param argument="--snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
+        <param argument="--snmeth" type="select" label="Function to calculate noise." help="" >
             <option value="median" selected="true">median</option>
             <option value="mean">mean</option>
             <!-- <option value="mad">mad</option> -->
         </param>
-        <param name="rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue="" 
-               label="Remove peaks that do not meet the filtering criteria. 
+        <param argument="--rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue=""
+               label="Remove peaks that do not meet the filtering criteria.
                       Otherwise peaks will be flagged instead."
                help="" />
     </inputs>
     <outputs>
-        <data name="filterFragSpectra_output_rdata" format="rdata" 
+        <data name="filterFragSpectra_output_rdata" format="rdata"
               label="${tool.name} on ${on_string}: RData" />
-        <data name="filterFragSpectra_output_prec_tsv" format="tsv" 
+        <data name="filterFragSpectra_output_prec_tsv" format="tsv"
               label="${tool.name} on ${on_string}: peaklist (precursors)" />
-        <data name="filterFragSpectra_output_frag_tsv" format="tsv" 
+        <data name="filterFragSpectra_output_frag_tsv" format="tsv"
               label="${tool.name} on ${on_string}: peaklist (fragments)" />
     </outputs>
     <tests>
         <test>
             <param name="pa" value="frag4feature_output.RData" />
-            <output name="filterFragSpectra_output_rdata" 
+            <output name="filterFragSpectra_output_rdata"
                     file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
-            <output name="filterFragSpectra_output_prec_tsv" 
+            <output name="filterFragSpectra_output_prec_tsv"
                     file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
-            <output name="filterFragSpectra_output_frag_tsv" 
+            <output name="filterFragSpectra_output_frag_tsv"
                     file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
         </test>
     </tests>