diff FeatureFinderMRM.xml @ 11:90f3670ec66b draft

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

--- a/FeatureFinderMRM.xml	Fri May 17 09:18:31 2019 -0400
+++ b/FeatureFinderMRM.xml	Thu Aug 27 19:41:29 2020 -0400
@@ -1,64 +1,78 @@
 <?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="FeatureFinderMRM" name="FeatureFinderMRM" version="2.3.0">
+<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Detects two-dimensional features in LC-MS data.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMRM</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[FeatureFinderMRM
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## 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 $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_algorithm_min_rt_distance:
-  -algorithm:min_rt_distance $param_algorithm_min_rt_distance
-#end if
-#if $param_algorithm_min_signal_to_noise_ratio:
-  -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
-  -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
-#end if
-    #if $adv_opts.param_algorithm_write_debug_files:
-  -algorithm:write_debug_files
-#end if
-    #if $adv_opts.param_algorithm_resample_traces:
-  -algorithm:resample_traces
-#end if
-    #if $adv_opts.param_algorithm_write_debuginfo:
-  -algorithm:write_debuginfo
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${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 file" help="(-in) "/>
-    <param name="param_algorithm_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds" help="(-min_rt_distance) "/>
-    <param name="param_algorithm_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise"/>
-    <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) "/>
-      <param name="param_algorithm_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature) "/>
-      <param name="param_algorithm_write_debug_files" display="radio" type="boolean" truevalue="-algorithm:write_debug_files" falsevalue="" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files) "/>
-      <param name="param_algorithm_resample_traces" display="radio" type="boolean" truevalue="-algorithm:resample_traces" falsevalue="" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces) "/>
-      <param name="param_algorithm_write_debuginfo" display="radio" type="boolean" truevalue="-algorithm:write_debuginfo" falsevalue="" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy" help="(-write_debuginfo) "/>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <section name="algorithm" title="Algorithm section" help="" expanded="false">
+      <param name="min_rt_distance" argument="-algorithm:min_rt_distance" type="float" optional="true" min="0.0" value="10.0" label="Minimal distance of MRM features in seconds" help=""/>
+      <param name="min_num_peaks_per_feature" argument="-algorithm:min_num_peaks_per_feature" type="integer" optional="true" min="1" value="5" label="Minimal number of peaks which are needed for a single feature" help=""/>
+      <param name="min_signal_to_noise_ratio" argument="-algorithm:min_signal_to_noise_ratio" type="float" optional="true" min="0.0" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="Set to zero if the MRM-traces contains mostly signals, and no noise"/>
+      <param name="write_debug_files" argument="-algorithm:write_debug_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help=""/>
+      <param name="resample_traces" argument="-algorithm:resample_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help=""/>
+      <param name="write_debuginfo" argument="-algorithm:write_debuginfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, debug messages are written, the output can be somewhat lengthy" help=""/>
+    </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="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </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>Detects two-dimensional features in LC-MS data.
+  <tests>
+    <expand macro="autotest_FeatureFinderMRM"/>
+    <expand macro="manutest_FeatureFinderMRM"/>
+  </tests>
+  <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMRM.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderMRM.html]]></help>
+  <expand macro="references"/>
 </tool>