--- a/EICExtractor.xml	Fri Nov 06 20:20:11 2020 +0000
+++ b/EICExtractor.xml	Thu Dec 01 19:23:24 2022 +0000
@@ -1,13 +1,11 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
-<tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Extracts intensities from dedicates positions in a LC/MS map</description>
   <macros>
     <token name="@EXECUTABLE@">EICExtractor</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,11 +14,21 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
-#if $in_header:
-  mkdir in_header &&
-  ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) }
+mkdir in_cond.in &&
+#if $in_cond.in_select == "no"
+mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
+${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
+#if $in_header_cond.in_header:
+  mkdir in_header_cond.in_header &&
+  #if $in_header_cond.in_header_select == "no"
+  mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} && 
+  ${' '.join(["ln -s '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
+  #else
+  ln -s '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' &&
+  #end if
 #end if
 mkdir pos &&
 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
@@ -36,10 +44,18 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
-#if $in_header:
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
+#if $in_header_cond.in_header:
   -in_header
-  ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])}
+  #if $in_header_cond.in_header_select == "no"
+  ${' '.join(["'in_header_cond.in_header/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
+  #else
+  'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)'
+  #end if
 #end if
 -pos
 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)'
@@ -66,24 +82,46 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/>
-    <param name="in_header" argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
-    <param name="pos" argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
-    <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
-    <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
-    <param name="rt_collect" argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <option value="no">No: process all datasets jointly</option>
+        <option value="yes">Yes: process each dataset in an independent job</option>
+      </param>
+      <when value="no">
+        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/>
+      </when>
+    </conditional>
+    <conditional name="in_header_cond">
+      <param name="in_header_select" type="select" label="Run tool in batch mode for -in_header">
+        <option value="no">No: process all datasets jointly</option>
+        <option value="yes">Yes: process each dataset in an independent job</option>
+      </param>
+      <when value="no">
+        <param argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in_header" type="data" format="txt" multiple="false" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
+    <param argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
+    <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
+    <param argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
     <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false">
       <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/>
       <param name="FHWM" argument="-auto_rt:FHWM" type="float" optional="true" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/>
       <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" optional="true" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="out_separator" argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help="">
+        <expand macro="list_string_san" name="out_separator"/>
       </param>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -100,13 +138,16 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_EICExtractor"/>
-    <expand macro="manutest_EICExtractor"/>
-  </tests>
+  <tests><test expect_num_outputs="1"><!-- just using some random test data -->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" value="spectra.mzML"/>
+    <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
+    <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
+  </test>
+</tests>
   <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_EICExtractor.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_EICExtractor.html]]></help>
   <expand macro="references"/>
 </tool>