diff OpenSwathMzMLFileCacher.xml @ 13:f82b320ceb90 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- a/OpenSwathMzMLFileCacher.xml	Fri Nov 06 19:51:52 2020 +0000
+++ b/OpenSwathMzMLFileCacher.xml	Thu Dec 01 19:04:12 2022 +0000
@@ -1,13 +1,11 @@
 <?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]-->
-<tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<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>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,21 +39,21 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
-    <param name="out_type" 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" 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">
       <option value="mzML">mzml</option>
       <option value="sqMass">sqmass</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param name="lossy_compression" 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 name="full_meta" 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=""/>
+    <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 name="lossy_mass_accuracy" 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 name="process_lowmemory" 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 name="lowmem_batchsize" argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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 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="-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="-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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -63,9 +61,8 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out">
+    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml">
       <change_format>
-        <when input="out_type" value="mzML" format="mzml"/>
         <when input="out_type" value="sqMass" format="sqmass"/>
       </change_format>
     </data>
@@ -73,13 +70,220 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_OpenSwathMzMLFileCacher"/>
-    <expand macro="manutest_OpenSwathMzMLFileCacher"/>
+  <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 -->
+    <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="OpenSwathMzMLFileCacher_1_input.mzML"/>
+      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 -->
+    <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="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"/>
+      <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>
+    </test>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 -->
+    <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="OpenSwathMzMLFileCacher_1_input.mzML"/>
+      <output name="out" file="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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 -->
+    <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="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
+      <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 -->
+    <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="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
+      <output name="out" file="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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 -->
+    <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="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
+      <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="true"/>
+        <param name="lowmem_batchsize" value="500"/>
+        <param name="force" value="false"/>
+        <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"/>
+      <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>
+    </test>
+    <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 -->
+    <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" file="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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 -->
+    <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_1_input_chrom.mzML"/>
+      <output name="out" file="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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathWorkflow_14_step2 -->
+    <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_14.chrom.tmp.sqMass"/>
+      <output name="out" file="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"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </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/2.6.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help>
   <expand macro="references"/>
 </tool>