diff FeatureFinderSuperHirn.xml @ 11:c42075bb5123 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"

--- a/FeatureFinderSuperHirn.xml	Fri May 17 09:26:00 2019 -0400
+++ b/FeatureFinderSuperHirn.xml	Thu Sep 03 16:16:49 2020 +0000
@@ -1,177 +1,109 @@
 <?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="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.3.0">
+<tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Finds mass spectrometric features in mass spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderSuperHirn</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[FeatureFinderSuperHirn
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_algorithm_centroiding_active:
-  -algorithm:centroiding:active
-#end if
-#if $param_algorithm_centroiding_window_width:
-  -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width
-#end if
-#if $param_algorithm_centroiding_absolute_isotope_mass_precision:
-  -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision
-#end if
-#if $param_algorithm_centroiding_relative_isotope_mass_precision:
-  -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision
-#end if
-#if $param_algorithm_centroiding_minimal_peak_height:
-  -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height
-#end if
-#if $param_algorithm_centroiding_min_ms_signal_intensity:
-  -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity
-#end if
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("featurexml")}'
 
-#if $rep_param_algorithm_ms1_precursor_detection_scan_levels:
--algorithm:ms1:precursor_detection_scan_levels
-  #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels:
-    #if " " in str(token):
-      "$token.param_algorithm_ms1_precursor_detection_scan_levels"
-    #else
-      $token.param_algorithm_ms1_precursor_detection_scan_levels
-    #end if
-  #end for
-#end if
-#if $param_algorithm_ms1_max_inter_scan_distance:
-  -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance
-#end if
-#if $param_algorithm_ms1_tr_resolution:
-  -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution
-#end if
-#if $param_algorithm_ms1_intensity_threshold:
-  -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold
-#end if
-#if $param_algorithm_ms1_max_inter_scan_rt_distance:
-  -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance
-#end if
-#if $param_algorithm_ms1_min_nb_cluster_members:
-  -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members
-#end if
-#if $param_algorithm_ms1_detectable_isotope_factor:
-  -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor
-#end if
-#if $param_algorithm_ms1_intensity_cv:
-  -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv
-#end if
-#if $param_algorithm_ms1_retention_time_tolerance:
-  -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance
-#end if
-#if $param_algorithm_ms1_mz_tolerance:
-  -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance
-#end if
-#if $param_algorithm_ms1_feature_merger_active:
-  -algorithm:ms1_feature_merger:active
-  #if " " in str($param_algorithm_ms1_feature_merger_active):
-    "$param_algorithm_ms1_feature_merger_active"
-  #else
-    $param_algorithm_ms1_feature_merger_active
-  #end if
-#end if
-#if $param_algorithm_ms1_feature_merger_tr_resolution:
-  -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
-#end if
-#if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
-  -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
-#end if
-#if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
-  -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
-#end if
-#if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
-  -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
-#end if
-#if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
-  -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
-#end if
-#if $param_algorithm_ms1_feature_selection_options_start_elution_window:
-  -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
-#end if
-#if $param_algorithm_ms1_feature_selection_options_end_elution_window:
-  -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
-#end if
-#if $param_algorithm_ms1_feature_selection_options_mz_range_min:
-  -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
-#end if
-#if $param_algorithm_ms1_feature_selection_options_mz_range_max:
-  -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
-#end if
-#if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
-  -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
-#end if
-#if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
-  -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("featurexml")}' '$out'
+#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="mzml" optional="False" label="input profile data file" help="(-in) "/>
-    <param name="param_algorithm_centroiding_active" display="radio" type="boolean" truevalue="-algorithm:centroiding:active" falsevalue="" checked="false" optional="True" label="MS1 data centroid data" help="(-active) "/>
-    <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/>
-    <param name="param_algorithm_centroiding_absolute_isotope_mass_precision" type="float" min="0.0" optional="True" value="0.01" label="Absolute isotope mass precision (Da)" help="(-absolute_isotope_mass_precision) "/>
-    <param name="param_algorithm_centroiding_relative_isotope_mass_precision" type="float" min="0.0" optional="True" value="10.0" label="Relative isotope mass precision" help="(-relative_isotope_mass_precision) "/>
-    <param name="param_algorithm_centroiding_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height) "/>
-    <param name="param_algorithm_centroiding_min_ms_signal_intensity" type="float" min="0.0" optional="True" value="50.0" label="Minimal Centroid MS Signal Intensity" help="(-min_ms_signal_intensity) "/>
-    <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels">
-      <param name="param_algorithm_ms1_precursor_detection_scan_levels" type="text" size="30" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels) ">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <section name="centroiding" title="" help="" expanded="false">
+        <param name="active" argument="-algorithm:centroiding:active" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MS1 data centroid data" help=""/>
+        <param name="window_width" argument="-algorithm:centroiding:window_width" type="integer" optional="true" min="1" value="5" label="Centroid window width" help=""/>
+        <param name="absolute_isotope_mass_precision" argument="-algorithm:centroiding:absolute_isotope_mass_precision" type="float" optional="true" min="0.0" value="0.01" label="Absolute isotope mass precision (Da)" help=""/>
+        <param name="relative_isotope_mass_precision" argument="-algorithm:centroiding:relative_isotope_mass_precision" type="float" optional="true" min="0.0" value="10.0" label="Relative isotope mass precision" help=""/>
+        <param name="minimal_peak_height" argument="-algorithm:centroiding:minimal_peak_height" type="float" optional="true" min="0.0" value="0.0" label="Minimal peak height" help=""/>
+        <param name="min_ms_signal_intensity" argument="-algorithm:centroiding:min_ms_signal_intensity" type="float" optional="true" min="0.0" value="50.0" label="Minimal Centroid MS Signal Intensity" help=""/>
+      </section>
+      <section name="ms1" title="" help="" expanded="false">
+        <param name="precursor_detection_scan_levels" argument="-algorithm:ms1:precursor_detection_scan_levels" type="text" optional="true" value="1" label="Precursor detection scan levels" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+          <expand macro="list_integer_valsan"/>
+        </param>
+        <param name="max_inter_scan_distance" argument="-algorithm:ms1:max_inter_scan_distance" type="integer" optional="true" min="0" value="0" label="MS1 max inter scan distance" help=""/>
+        <param name="tr_resolution" argument="-algorithm:ms1:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/>
+        <param name="intensity_threshold" argument="-algorithm:ms1:intensity_threshold" type="float" optional="true" min="0.0" value="1000.0" label="FT peak detect MS1 intensity min threshold" help=""/>
+        <param name="max_inter_scan_rt_distance" argument="-algorithm:ms1:max_inter_scan_rt_distance" type="float" optional="true" min="0.0" value="0.1" label="MS1 max inter scan distance" help=""/>
+        <param name="min_nb_cluster_members" argument="-algorithm:ms1:min_nb_cluster_members" type="integer" optional="true" min="0" value="4" label="FT peak detect MS1 min nb peak members" help=""/>
+        <param name="detectable_isotope_factor" argument="-algorithm:ms1:detectable_isotope_factor" type="float" optional="true" min="0.0" value="0.05" label="Detectable isotope facto" help=""/>
+        <param name="intensity_cv" argument="-algorithm:ms1:intensity_cv" type="float" optional="true" min="0.0" value="0.9" label="IntensityCV" help=""/>
+        <param name="retention_time_tolerance" argument="-algorithm:ms1:retention_time_tolerance" type="float" optional="true" min="0.0" value="0.5" label="MS1 retention time tolerance (minutes)" help=""/>
+        <param name="mz_tolerance" argument="-algorithm:ms1:mz_tolerance" type="float" optional="true" min="0.0" value="0.0" label="MS1 m/z tolerance (ppm)" help=""/>
+      </section>
+      <section name="ms1_feature_merger" title="" help="" expanded="false">
+        <param name="active" argument="-algorithm:ms1_feature_merger:active" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Activation of MS1 feature merging post processing" help=""/>
+        <param name="tr_resolution" argument="-algorithm:ms1_feature_merger:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/>
+        <param name="initial_apex_tr_tolerance" argument="-algorithm:ms1_feature_merger:initial_apex_tr_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Initial Apex Tr tolerance" help=""/>
+        <param name="feature_merging_tr_tolerance" argument="-algorithm:ms1_feature_merger:feature_merging_tr_tolerance" type="float" optional="true" min="0.0" value="1.0" label="MS1 feature Tr merging tolerance" help=""/>
+        <param name="intensity_variation_percentage" argument="-algorithm:ms1_feature_merger:intensity_variation_percentage" type="float" optional="true" min="0.0" max="100.0" value="25.0" label="Percentage of intensity variation between LC border peaks" help=""/>
+        <param name="ppm_tolerance_for_mz_clustering" argument="-algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering" type="float" optional="true" min="0.0" value="10.0" label="PPM value for the m/z clustering of merging candidates" help=""/>
+      </section>
+      <section name="ms1_feature_selection_options" title="" help="" expanded="false">
+        <param name="start_elution_window" argument="-algorithm:ms1_feature_selection_options:start_elution_window" type="float" optional="true" min="0.0" value="0.0" label="start elution window (minutes)" help=""/>
+        <param name="end_elution_window" argument="-algorithm:ms1_feature_selection_options:end_elution_window" type="float" optional="true" min="0.0" value="180.0" label="end elution window (minutes)" help=""/>
+        <param name="mz_range_min" argument="-algorithm:ms1_feature_selection_options:mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="MS1 feature mz range min" help=""/>
+        <param name="mz_range_max" argument="-algorithm:ms1_feature_selection_options:mz_range_max" type="float" optional="true" min="0.0" value="2000.0" label="MS1 feature mz range max" help=""/>
+        <param name="chrg_range_min" argument="-algorithm:ms1_feature_selection_options:chrg_range_min" type="integer" optional="true" min="0" value="1" label="MS1 feature CHRG range min" help=""/>
+        <param name="chrg_range_max" argument="-algorithm:ms1_feature_selection_options:chrg_range_max" type="integer" optional="true" min="0" value="5" label="MS1 feature CHRG range max" help=""/>
+      </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>
-    </repeat>
-    <param name="param_algorithm_ms1_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance) "/>
-    <param name="param_algorithm_ms1_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/>
-    <param name="param_algorithm_ms1_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold) "/>
-    <param name="param_algorithm_ms1_max_inter_scan_rt_distance" type="float" min="0.0" optional="True" value="0.1" label="MS1 max inter scan distance" help="(-max_inter_scan_rt_distance) "/>
-    <param name="param_algorithm_ms1_min_nb_cluster_members" type="integer" min="0" optional="True" value="4" label="FT peak detect MS1 min nb peak members" help="(-min_nb_cluster_members) "/>
-    <param name="param_algorithm_ms1_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope facto" help="(-detectable_isotope_factor) "/>
-    <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/>
-    <param name="param_algorithm_ms1_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance) "/>
-    <param name="param_algorithm_ms1_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance) "/>
-    <param name="param_algorithm_ms1_feature_merger_active" display="radio" type="select" optional="False" value="true" label="Activation of MS1 feature merging post processing" help="(-active) ">
-      <option value="true" selected="true">true</option>
-      <option value="false">false</option>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
-    <param name="param_algorithm_ms1_feature_merger_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/>
-    <param name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance) "/>
-    <param name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" type="float" min="0.0" optional="True" value="1.0" label="MS1 feature Tr merging tolerance" help="(-feature_merging_tr_tolerance) "/>
-    <param name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" type="float" min="0.0" max="100.0" optional="True" value="25.0" label="Percentage of intensity variation between LC border peaks" help="(-intensity_variation_percentage) "/>
-    <param name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" type="float" min="0.0" optional="True" value="10.0" label="PPM value for the m/z clustering of merging candidates" help="(-ppm_tolerance_for_mz_clustering) "/>
-    <param name="param_algorithm_ms1_feature_selection_options_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window) "/>
-    <param name="param_algorithm_ms1_feature_selection_options_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window) "/>
-    <param name="param_algorithm_ms1_feature_selection_options_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min) "/>
-    <param name="param_algorithm_ms1_feature_selection_options_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max) "/>
-    <param name="param_algorithm_ms1_feature_selection_options_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min) "/>
-    <param name="param_algorithm_ms1_feature_selection_options_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max) "/>
-    <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" format="featurexml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Finds mass spectrometric features in mass spectra.
+  <tests>
+    <expand macro="autotest_FeatureFinderSuperHirn"/>
+    <expand macro="manutest_FeatureFinderSuperHirn"/>
+  </tests>
+  <help><![CDATA[Finds mass spectrometric features in mass spectra.
 
-
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderSuperHirn.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_FeatureFinderSuperHirn.html]]></help>
+  <expand macro="references"/>
 </tool>