--- a/MapAlignerPoseClustering.xml	Fri Nov 06 19:57:49 2020 +0000
+++ b/MapAlignerPoseClustering.xml	Thu Dec 01 19:16:48 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: [Map Alignment]-->
-<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,13 +14,20 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in 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($in_cond.in.ext)' &&
+#end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
+  mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
+  mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
 #end if
 #if $reference.file:
   mkdir reference.file &&
@@ -36,14 +41,18 @@
 python3 '$__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 $in_cond.in_select == "no"
+${' '.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($in_cond.in.ext)'
+#end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
-  ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
+  ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), f.ext) for i, f in enumerate($in_cond.in) if f])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
-  ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+  ${' '.join(["'trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])}
 #end if
 #if $reference.file:
   -reference:file
@@ -55,7 +64,7 @@
 
 ## Postprocessing
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
+  ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -65,7 +74,18 @@
     <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="featurexml,mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
+    <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="featurexml,mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="featurexml,mzml" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
+      </when>
+    </conditional>
     <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
       <param name="file" argument="-reference:file" type="data" format="featurexml,mzml" optional="true" label="File to use as reference (same file format as input files required)" help=" select featurexml,mzml data sets(s)"/>
       <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
@@ -81,10 +101,10 @@
         <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" optional="true" min="0.0" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="This applies for both directions"/>
         <param name="max_scaling" argument="-algorithm:superimposer:max_scaling" type="float" optional="true" min="1.0" value="2.0" label="Maximal scaling which is considered during histogramming" help="The minimal scaling is the reciprocal of this"/>
         <param name="dump_buckets" argument="-algorithm:superimposer:dump_buckets" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="A serial number for each invocation will be appended automatically">
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="dump_buckets"/>
         </param>
         <param name="dump_pairs" argument="-algorithm:superimposer:dump_pairs" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="A serial number for each invocation will be appended automatically">
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="dump_pairs"/>
         </param>
       </section>
       <section name="pairfinder" title="" help="" expanded="false">
@@ -99,10 +119,10 @@
         </section>
         <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
           <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-          <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
+          <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
             <option value="Da" selected="true">Da</option>
             <option value="ppm">ppm</option>
-            <expand macro="list_string_san"/>
+            <expand macro="list_string_san" name="unit"/>
           </param>
           <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
           <param name="weight" argument="-algorithm:pairfinder:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
@@ -110,18 +130,18 @@
         <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
           <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
           <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-          <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+          <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
             <option value="enabled">enabled</option>
             <option value="disabled" selected="true">disabled</option>
-            <expand macro="list_string_san"/>
+            <expand macro="list_string_san" name="log_transform"/>
           </param>
         </section>
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <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">
@@ -132,11 +152,11 @@
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" pattern="__name_and_ext__"/>
+      <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
-      <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
+      <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
@@ -146,13 +166,236 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MapAlignerPoseClustering"/>
-    <expand macro="manutest_MapAlignerPoseClustering"/>
+  <tests><!-- TOPP_MapAlignerPoseClustering_1 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
+      </conditional>
+      <output_collection name="out" count="3"/>
+      <output_collection name="trafo_out" count="3"/>
+      <section name="reference">
+        <param name="index" value="0"/>
+      </section>
+      <section name="algorithm">
+        <param name="max_num_peaks_considered" value="400"/>
+        <section name="superimposer">
+          <param name="mz_pair_max_distance" value="0.5"/>
+          <param name="rt_pair_distance_fraction" value="0.1"/>
+          <param name="num_used_points" value="2000"/>
+          <param name="scaling_bucket_size" value="0.005"/>
+          <param name="shift_bucket_size" value="3.0"/>
+          <param name="max_shift" value="1000.0"/>
+          <param name="max_scaling" value="2.0"/>
+          <param name="dump_buckets" value=""/>
+          <param name="dump_pairs" value=""/>
+        </section>
+        <section name="pairfinder">
+          <param name="second_nearest_gap" value="2.0"/>
+          <param name="use_identifications" value="false"/>
+          <param name="ignore_charge" value="true"/>
+          <param name="ignore_adduct" value="true"/>
+          <section name="distance_RT">
+            <param name="max_difference" value="30.0"/>
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_MZ">
+            <param name="max_difference" value="0.3"/>
+            <param name="unit" value="Da"/>
+            <param name="exponent" value="2.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_intensity">
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="0.0"/>
+            <param name="log_transform" value="disabled"/>
+          </section>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_MapAlignerPoseClustering_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
+      </conditional>
+      <output_collection name="out" count="3"/>
+      <section name="reference">
+        <param name="index" value="0"/>
+      </section>
+      <section name="algorithm">
+        <param name="max_num_peaks_considered" value="400"/>
+        <section name="superimposer">
+          <param name="mz_pair_max_distance" value="0.5"/>
+          <param name="rt_pair_distance_fraction" value="0.1"/>
+          <param name="num_used_points" value="2000"/>
+          <param name="scaling_bucket_size" value="0.005"/>
+          <param name="shift_bucket_size" value="3.0"/>
+          <param name="max_shift" value="1000.0"/>
+          <param name="max_scaling" value="2.0"/>
+          <param name="dump_buckets" value=""/>
+          <param name="dump_pairs" value=""/>
+        </section>
+        <section name="pairfinder">
+          <param name="second_nearest_gap" value="2.0"/>
+          <param name="use_identifications" value="false"/>
+          <param name="ignore_charge" value="false"/>
+          <param name="ignore_adduct" value="true"/>
+          <section name="distance_RT">
+            <param name="max_difference" value="100.0"/>
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_MZ">
+            <param name="max_difference" value="0.3"/>
+            <param name="unit" value="Da"/>
+            <param name="exponent" value="2.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_intensity">
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="0.0"/>
+            <param name="log_transform" value="disabled"/>
+          </section>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_MapAlignerPoseClustering_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
+      </conditional>
+      <output_collection name="out" count="2"/>
+      <section name="reference">
+        <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
+        <param name="index" value="0"/>
+      </section>
+      <section name="algorithm">
+        <param name="max_num_peaks_considered" value="400"/>
+        <section name="superimposer">
+          <param name="mz_pair_max_distance" value="0.5"/>
+          <param name="rt_pair_distance_fraction" value="0.1"/>
+          <param name="num_used_points" value="2000"/>
+          <param name="scaling_bucket_size" value="0.005"/>
+          <param name="shift_bucket_size" value="3.0"/>
+          <param name="max_shift" value="1000.0"/>
+          <param name="max_scaling" value="2.0"/>
+          <param name="dump_buckets" value=""/>
+          <param name="dump_pairs" value=""/>
+        </section>
+        <section name="pairfinder">
+          <param name="second_nearest_gap" value="2.0"/>
+          <param name="use_identifications" value="false"/>
+          <param name="ignore_charge" value="true"/>
+          <param name="ignore_adduct" value="true"/>
+          <section name="distance_RT">
+            <param name="max_difference" value="30.0"/>
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_MZ">
+            <param name="max_difference" value="0.3"/>
+            <param name="unit" value="Da"/>
+            <param name="exponent" value="2.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_intensity">
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="0.0"/>
+            <param name="log_transform" value="disabled"/>
+          </section>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_MapAlignerPoseClustering_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
+      </conditional>
+      <output_collection name="trafo_out" count="2"/>
+      <section name="reference">
+        <param name="index" value="2"/>
+      </section>
+      <section name="algorithm">
+        <param name="max_num_peaks_considered" value="400"/>
+        <section name="superimposer">
+          <param name="mz_pair_max_distance" value="0.5"/>
+          <param name="rt_pair_distance_fraction" value="0.1"/>
+          <param name="num_used_points" value="2000"/>
+          <param name="scaling_bucket_size" value="0.005"/>
+          <param name="shift_bucket_size" value="3.0"/>
+          <param name="max_shift" value="1000.0"/>
+          <param name="max_scaling" value="2.0"/>
+          <param name="dump_buckets" value=""/>
+          <param name="dump_pairs" value=""/>
+        </section>
+        <section name="pairfinder">
+          <param name="second_nearest_gap" value="2.0"/>
+          <param name="use_identifications" value="false"/>
+          <param name="ignore_charge" value="true"/>
+          <param name="ignore_adduct" value="true"/>
+          <section name="distance_RT">
+            <param name="max_difference" value="30.0"/>
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_MZ">
+            <param name="max_difference" value="0.3"/>
+            <param name="unit" value="Da"/>
+            <param name="exponent" value="2.0"/>
+            <param name="weight" value="1.0"/>
+          </section>
+          <section name="distance_intensity">
+            <param name="exponent" value="1.0"/>
+            <param name="weight" value="0.0"/>
+            <param name="log_transform" value="disabled"/>
+          </section>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
   <expand macro="references"/>
 </tool>