diff MapAlignerPoseClustering.xml @ 11:e527a8a430dd draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

--- a/MapAlignerPoseClustering.xml	Thu Dec 01 19:16:48 2022 +0000
+++ b/MapAlignerPoseClustering.xml	Fri Jun 14 21:40:41 2024 +0000
@@ -1,8 +1,7 @@
-<?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@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
+  <description>Corrects retention time distortions between maps using a pose clustering approach</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 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])}
+${' '.join(["cp '%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($in_cond.in.ext)' &&
+cp '$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 &&
@@ -31,7 +30,7 @@
 #end if
 #if $reference.file:
   mkdir reference.file &&
-  ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
+  cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
 #end if
 
 ## Main program call
@@ -80,26 +79,26 @@
         <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)"/>
+        <param argument="-in" type="data" format="featurexml,mzml" multiple="true" 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)"/>
+        <param argument="-in" type="data" format="featurexml,mzml" 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"/>
+      <param name="index" argument="-reference:index" type="integer" 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="max_num_peaks_considered" argument="-algorithm:max_num_peaks_considered" type="integer" optional="true" min="-1" value="1000" label="The maximal number of peaks/features to be considered per map" help="To use all, set to '-1'"/>
+      <param name="max_num_peaks_considered" argument="-algorithm:max_num_peaks_considered" type="integer" min="-1" value="1000" label="The maximal number of peaks/features to be considered per map" help="To use all, set to '-1'"/>
       <section name="superimposer" title="" help="" expanded="false">
-        <param name="mz_pair_max_distance" argument="-algorithm:superimposer:mz_pair_max_distance" type="float" optional="true" min="0.0" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="This condition applies to the pairs considered in hashing"/>
-        <param name="rt_pair_distance_fraction" argument="-algorithm:superimposer:rt_pair_distance_fraction" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval" help="(i.e., max - min).  "/>
-        <param name="num_used_points" argument="-algorithm:superimposer:num_used_points" type="integer" optional="true" min="-1" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1"/>
-        <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" optional="true" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
-        <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" optional="true" min="0.0" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be about the time between consecutive MS scans"/>
-        <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="mz_pair_max_distance" argument="-algorithm:superimposer:mz_pair_max_distance" type="float" min="0.0" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="This condition applies to the pairs considered in hashing"/>
+        <param name="rt_pair_distance_fraction" argument="-algorithm:superimposer:rt_pair_distance_fraction" type="float" min="0.0" max="1.0" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval" help="(i.e., max - min).  "/>
+        <param name="num_used_points" argument="-algorithm:superimposer:num_used_points" type="integer" min="-1" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1"/>
+        <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
+        <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" min="0.0" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be about the time between consecutive MS scans"/>
+        <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" 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" 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" name="dump_buckets"/>
         </param>
@@ -108,29 +107,29 @@
         </param>
       </section>
       <section name="pairfinder" title="" help="" expanded="false">
-        <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
+        <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
         <param name="use_identifications" argument="-algorithm:pairfinder:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/>
         <param name="ignore_charge" argument="-algorithm:pairfinder:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
         <param name="ignore_adduct" argument="-algorithm:pairfinder:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
         <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
-          <param name="max_difference" argument="-algorithm:pairfinder:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
-          <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') 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_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+          <param name="max_difference" argument="-algorithm:pairfinder:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
+          <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') 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_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
         </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" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
+          <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" 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" type="select" 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" 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=""/>
+          <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" 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" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
         </section>
         <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" 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))">
+          <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" 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" 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" type="select" 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" name="log_transform"/>
@@ -140,7 +139,7 @@
     </section>
     <expand macro="adv_opts_macro">
       <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="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -166,7 +165,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapAlignerPoseClustering_1 -->
+  <tests>
+    <!-- TOPP_MapAlignerPoseClustering_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -222,6 +222,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerPoseClustering_2 -->
     <test expect_num_outputs="2">
@@ -278,6 +281,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerPoseClustering_3 -->
     <test expect_num_outputs="2">
@@ -335,6 +341,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerPoseClustering_4 -->
     <test expect_num_outputs="2">
@@ -391,11 +400,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </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/2.8.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
   <expand macro="references"/>
 </tool>