--- a/MapAlignerIdentification.xml	Fri May 17 10:18:39 2019 -0400
+++ b/MapAlignerIdentification.xml	Wed Sep 09 19:44:14 2020 +0000
@@ -1,212 +1,202 @@
 <?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="MapAlignerIdentification" name="MapAlignerIdentification" version="2.3.0">
+<tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerIdentification</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[MapAlignerIdentification
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
+## Preprocessing
+mkdir in &&
+${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out &&
+#end if
+#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir trafo_out &&
+#end if
+#if $design:
+  mkdir design &&
+  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+#end if
+#if $reference.file:
+  mkdir reference.file &&
+  ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
+#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-  #for token in $param_in:
-    $token
-  #end for
-
-#if $rep_param_out:
--out
-  #for token in $rep_param_out:
-    #if " " in str(token):
-      "$token.param_out"
-    #else
-      $token.param_out
-    #end if
-  #end for
+${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out
+  ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
+#end if
+#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -trafo_out
+  ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+#end if
+#if $design:
+  -design
+  'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
+#end if
+#if $reference.file:
+  -reference:file
+  'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
 #end if
 
-#if $rep_param_trafo_out:
--trafo_out
-  #for token in $rep_param_trafo_out:
-    #if " " in str(token):
-      "$token.param_trafo_out"
-    #else
-      $token.param_trafo_out
-    #end if
-  #end for
-#end if
-#if $param_design:
-  -design $param_design
-#end if
-#if $param_reference_file:
-  -reference:file $param_reference_file
-#end if
-#if $param_reference_index:
-  -reference:index $param_reference_index
-#end if
-#if $param_algorithm_min_run_occur:
-  -algorithm:min_run_occur $param_algorithm_min_run_occur
-#end if
-#if $param_algorithm_max_rt_shift:
-  -algorithm:max_rt_shift $param_algorithm_max_rt_shift
-#end if
-#if $param_algorithm_use_unassigned_peptides:
-  -algorithm:use_unassigned_peptides
-  #if " " in str($param_algorithm_use_unassigned_peptides):
-    "$param_algorithm_use_unassigned_peptides"
-  #else
-    $param_algorithm_use_unassigned_peptides
-  #end if
-#end if
-#if $param_algorithm_use_feature_rt:
-  -algorithm:use_feature_rt
-#end if
-#if $param_model_type:
-  -model:type
-  #if " " in str($param_model_type):
-    "$param_model_type"
-  #else
-    $param_model_type
-  #end if
-#end if
-#if $param_model_linear_symmetric_regression:
-  -model:linear:symmetric_regression
-#end if
-#if $param_model_b_spline_wavelength:
-  -model:b_spline:wavelength $param_model_b_spline_wavelength
-#end if
-#if $param_model_b_spline_num_nodes:
-  -model:b_spline:num_nodes $param_model_b_spline_num_nodes
-#end if
-#if $param_model_b_spline_extrapolate:
-  -model:b_spline:extrapolate
-  #if " " in str($param_model_b_spline_extrapolate):
-    "$param_model_b_spline_extrapolate"
-  #else
-    $param_model_b_spline_extrapolate
-  #end if
-#end if
-#if $param_model_b_spline_boundary_condition:
-  -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
-#end if
-#if $param_model_lowess_span:
-  -model:lowess:span $param_model_lowess_span
-#end if
-#if $param_model_lowess_num_iterations:
-  -model:lowess:num_iterations $param_model_lowess_num_iterations
-#end if
-#if $param_model_lowess_delta:
-  -model:lowess:delta $param_model_lowess_delta
-#end if
-#if $param_model_lowess_interpolation_type:
-  -model:lowess:interpolation_type
-  #if " " in str($param_model_lowess_interpolation_type):
-    "$param_model_lowess_interpolation_type"
-  #else
-    $param_model_lowess_interpolation_type
-  #end if
+## Postprocessing
+#if "trafo_out_FLAG" in str($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 _])}
 #end if
-#if $param_model_lowess_extrapolation_type:
-  -model:lowess:extrapolation_type
-  #if " " in str($param_model_lowess_extrapolation_type):
-    "$param_model_lowess_extrapolation_type"
-  #else
-    $param_model_lowess_extrapolation_type
-  #end if
-#end if
-#if $param_model_interpolated_interpolation_type:
-  -model:interpolated:interpolation_type
-  #if " " in str($param_model_interpolated_interpolation_type):
-    "$param_model_interpolated_interpolation_type"
-  #else
-    $param_model_interpolated_interpolation_type
-  #end if
-#end if
-#if $param_model_interpolated_extrapolation_type:
-  -model:interpolated:extrapolation_type
-  #if " " in str($param_model_interpolated_extrapolation_type):
-    "$param_model_interpolated_extrapolation_type"
-  #else
-    $param_model_interpolated_extrapolation_type
-  #end if
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_in" type="data" format="featurexml,consensusxml,idxml" multiple="true" optional="False" size="30" label="Input files to align (all must have the same file type)" help="(-in) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+    <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
+    <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="consensusxml,featurexml,idxml" optional="true" label="File to use as reference" help=" select consensusxml,featurexml,idxml 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"/>
+    </section>
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <param name="score_cutoff" argument="-algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If only IDs above a score cutoff should be used" help="Used together with min_score"/>
+      <param name="min_score" argument="-algorithm:min_score" type="float" optional="true" value="0.05" label="Minimum score for an ID to be considered" help="Applies to the last score calculated.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
+      <param name="min_run_occur" argument="-algorithm:min_run_occur" type="integer" optional="true" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
+      <param name="max_rt_shift" argument="-algorithm:max_rt_shift" type="float" optional="true" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
+      <param name="use_unassigned_peptides" argument="-algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
+      <param name="use_feature_rt" argument="-algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
+    </section>
+    <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
+      <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help="">
+        <option value="linear">linear</option>
+        <option value="b_spline" selected="true">b_spline</option>
+        <option value="lowess">lowess</option>
+        <option value="interpolated">interpolated</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
+        <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
+        <param name="x_weight" argument="-model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help="">
+          <option value="">default (nothing chosen)</option>
+          <option value="1/x">1/x</option>
+          <option value="1/x2">1/x2</option>
+          <option value="ln(x)">ln(x)</option>
+          <option value=""></option>
+          <expand macro="list_string_san"/>
+        </param>
+        <param name="y_weight" argument="-model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help="">
+          <option value="">default (nothing chosen)</option>
+          <option value="1/y">1/y</option>
+          <option value="1/y2">1/y2</option>
+          <option value="ln(y)">ln(y)</option>
+          <option value=""></option>
+          <expand macro="list_string_san"/>
+        </param>
+        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
+        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
+        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
+        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
+      </section>
+      <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
+        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
+        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" display="radio" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+          <option value="linear" selected="true">linear</option>
+          <option value="b_spline">b_spline</option>
+          <option value="constant">constant</option>
+          <option value="global_linear">global_linear</option>
+          <expand macro="list_string_san"/>
+        </param>
+        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
+      </section>
+      <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
+        <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+        <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" display="radio" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+          <option value="linear">linear</option>
+          <option value="cspline" selected="true">cspline</option>
+          <option value="akima">akima</option>
+          <expand macro="list_string_san"/>
+        </param>
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" display="radio" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+          <option value="two-point-linear">two-point-linear</option>
+          <option value="four-point-linear" selected="true">four-point-linear</option>
+          <option value="global-linear">global-linear</option>
+          <expand macro="list_string_san"/>
+        </param>
+      </section>
+      <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" display="radio" type="select" optional="false" label="Type of interpolation to apply" help="">
+          <option value="linear">linear</option>
+          <option value="cspline" selected="true">cspline</option>
+          <option value="akima">akima</option>
+          <expand macro="list_string_san"/>
+        </param>
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" display="radio" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+          <option value="two-point-linear" selected="true">two-point-linear</option>
+          <option value="four-point-linear">four-point-linear</option>
+          <option value="global-linear">global-linear</option>
+          <expand macro="list_string_san"/>
+        </param>
+      </section>
+    </section>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
+      <option value="out_FLAG">out (Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model)</option>
+      <option value="trafo_out_FLAG">trafo_out (Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model)</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
-    <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
-    <param name="param_reference_file" type="data" format="featurexml,consensusxml,idxml" optional="True" label="File to use as reference" help="(-file) "/>
-    <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
-    <param name="param_algorithm_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl" help="(-min_run_occur) reference, if any) in which a peptide must occur to be used for the alignment. &lt;br&gt;Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
-    <param name="param_algorithm_max_rt_shift" type="float" min="0.0" optional="True" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="(-max_rt_shift) reference). Peptides with higher shifts (outliers) are not used to compute the alignment. &lt;br&gt;If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
-    <param name="param_algorithm_use_unassigned_peptides" display="radio" type="select" optional="False" value="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps?" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used">
-      <option value="true" selected="true">true</option>
-      <option value="false">false</option>
-    </param>
-    <param name="param_algorithm_use_feature_rt" display="radio" type="boolean" truevalue="-algorithm:use_feature_rt" falsevalue="" checked="false" optional="True" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="(-use_feature_rt) If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. &lt;br&gt;Precludes 'use_unassigned_peptides'"/>
-    <param name="param_model_type" display="radio" type="select" optional="False" value="b_spline" label="Type of model" help="(-type) ">
-      <option value="linear">linear</option>
-      <option value="b_spline" selected="true">b_spline</option>
-      <option value="lowess">lowess</option>
-      <option value="interpolated">interpolated</option>
-    </param>
-    <param name="param_model_linear_symmetric_regression" display="radio" type="boolean" truevalue="-model:linear:symmetric_regression" falsevalue="" checked="false" optional="True" label="Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
-    <param name="param_model_b_spline_wavelength" type="float" min="0.0" optional="True" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
-    <param name="param_model_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for B-spline fitting" help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-    <param name="param_model_b_spline_extrapolate" display="radio" type="select" optional="False" value="linear" label="Method to use for extrapolation beyond the original data range" help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
-      <option value="linear" selected="true">linear</option>
-      <option value="b_spline">b_spline</option>
-      <option value="constant">constant</option>
-      <option value="global_linear">global_linear</option>
-    </param>
-    <param name="param_model_b_spline_boundary_condition" type="integer" min="0" max="2" optional="True" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help="(-boundary_condition) "/>
-    <param name="param_model_lowess_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="(-span) Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-    <param name="param_model_lowess_num_iterations" type="integer" min="0" optional="True" value="3" label="Number of robustifying iterations for lowess fitting" help="(-num_iterations) "/>
-    <param name="param_model_lowess_delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input," help="(-delta) e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-    <param name="param_model_lowess_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Method to use for interpolation between datapoints computed by lowess" help="(-interpolation_type) 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
-      <option value="linear">linear</option>
-      <option value="cspline" selected="true">cspline</option>
-      <option value="akima">akima</option>
-    </param>
-    <param name="param_model_lowess_extrapolation_type" display="radio" type="select" optional="False" value="four-point-linear" label="Method to use for extrapolation outside the data range" help="(-extrapolation_type) 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
-      <option value="two-point-linear">two-point-linear</option>
-      <option value="four-point-linear" selected="true">four-point-linear</option>
-      <option value="global-linear">global-linear</option>
-    </param>
-    <param name="param_model_interpolated_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) ">
-      <option value="linear">linear</option>
-      <option value="cspline" selected="true">cspline</option>
-      <option value="akima">akima</option>
-    </param>
-    <param name="param_model_interpolated_extrapolation_type" display="radio" type="select" optional="False" value="two-point-linear" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="(-extrapolation_type) Note that global-linear may not be continuous at the border">
-      <option value="two-point-linear" selected="true">two-point-linear</option>
-      <option value="four-point-linear">four-point-linear</option>
-      <option value="global-linear">global-linear</option>
-    </param>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_out" metadata_source="param_in" format="input"/>
-    <data name="param_trafo_out" format="trafoxml"/>
+    <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
+      <discover_datasets directory="out" pattern="__name_and_ext__"/>
+      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </collection>
+    <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
+      <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
+      <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </collection>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Corrects retention time distortions between maps based on common peptide identifications.
+  <tests>
+    <expand macro="autotest_MapAlignerIdentification"/>
+    <expand macro="manutest_MapAlignerIdentification"/>
+  </tests>
+  <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerIdentification.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_MapAlignerIdentification.html]]></help>
+  <expand macro="references"/>
 </tool>