Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher

diff OpenSwathMzMLFileCacher.xml @ 14:fe39f583c19a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:42:42 +0000
parents f82b320ceb90
children
line wrap: on
line diff
--- a/OpenSwathMzMLFileCacher.xml	Thu Dec 01 19:04:12 2022 +0000
+++ b/OpenSwathMzMLFileCacher.xml	Fri Jun 14 21:42:42 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: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description>
+  <description>This tool caches the spectra and chromatogram data of an mzML to disk</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,20 +38,21 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
+    <param argument="-in" type="data" format="mzml,sqmass" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
       <option value="mzML">mzml</option>
       <option value="sqMass">sqmass</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/>
     <param argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
+      <param argument="-lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
       <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
-      <param argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
+      <param argument="-lowmem_batchsize" type="integer" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
       <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>
@@ -70,7 +70,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 -->
+  <tests>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="lossy_mass_accuracy" value="-1.0"/>
@@ -80,7 +81,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_1_output_1.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -90,6 +91,9 @@
           <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_OpenSwathMzMLFileCacher_test_2_step1 -->
     <test expect_num_outputs="2">
@@ -101,7 +105,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_2_output_1.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -111,6 +115,9 @@
           <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_OpenSwathMzMLFileCacher_test_3_step1 -->
     <test expect_num_outputs="2">
@@ -122,7 +129,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
       <param name="out_type" value="sqMass"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -132,6 +139,9 @@
           <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_OpenSwathMzMLFileCacher_test_3_step2 -->
     <test expect_num_outputs="2">
@@ -143,7 +153,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -153,6 +163,9 @@
           <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_OpenSwathMzMLFileCacher_test_4_step1 -->
     <test expect_num_outputs="2">
@@ -164,7 +177,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
       <param name="out_type" value="sqMass"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -174,6 +187,9 @@
           <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_OpenSwathMzMLFileCacher_test_4_step2 -->
     <test expect_num_outputs="2">
@@ -185,7 +201,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -195,6 +211,9 @@
           <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_OpenSwathMzMLFileCacher_test_5_step1 -->
     <test expect_num_outputs="2">
@@ -206,7 +225,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_1_output_1.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -216,6 +235,33 @@
           <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_OpenSwathAnalyzer_test_3_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="lowmem_batchsize" value="500"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
+      <output name="out" value="OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
+      <param name="out_type" value="mzML"/>
+      <param name="lossy_compression" value="true"/>
+      <param name="full_meta" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <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_OpenSwathAnalyzer_test_4_prepare1 -->
     <test expect_num_outputs="2">
@@ -227,7 +273,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -237,6 +283,9 @@
           <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_OpenSwathAnalyzer_test_4_prepare2 -->
     <test expect_num_outputs="2">
@@ -248,7 +297,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -258,6 +307,9 @@
           <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_OpenSwathWorkflow_14_step2 -->
     <test expect_num_outputs="2">
@@ -269,7 +321,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
-      <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="false"/>
       <param name="full_meta" value="false"/>
@@ -279,11 +331,38 @@
           <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_OpenSwathWorkflow_16_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="lossy_mass_accuracy" value="0.0001"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="lowmem_batchsize" value="500"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+      <output name="out" value="OpenSwathWorkflow_16_input.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <param name="out_type" value="sqMass"/>
+      <param name="lossy_compression" value="true"/>
+      <param name="full_meta" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <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[This tool caches the spectra and chromatogram data of an mzML to disk.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathMzMLFileCacher.html]]></help>
   <expand macro="references"/>
 </tool>