diff OpenSwathChromatogramExtractor.xml @ 13:f78d734b7c01 draft default tip

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

--- a/OpenSwathChromatogramExtractor.xml	Fri Nov 06 19:56:22 2020 +0000
+++ b/OpenSwathChromatogramExtractor.xml	Thu Dec 01 19:13:34 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="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Extract chromatograms (XIC) from a MS2 map file.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,8 +14,13 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+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])}
+#else
+ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
 mkdir tr &&
 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $rt_norm:
@@ -33,7 +36,11 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
 -tr
 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
 #if $rt_norm:
@@ -53,35 +60,46 @@
     <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" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
-    <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
-    <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
-    <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
-    <param name="rt_window" argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
-    <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
-    <param name="mz_window" argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
-    <param name="ppm" argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
-    <param name="is_swath" argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
-    <param name="extract_MS1" argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <option value="no">No: process all datasets jointly</option>
+        <option value="yes">Yes: process each dataset in an independent job</option>
+      </param>
+      <when value="no">
+        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
+    <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
+    <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
+    <param argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
+    <param argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
+    <param argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
+    <param argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
+    <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
+    <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
         <option value="linear" selected="true">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="interpolated">interpolated</option>
         <option value="lowess">lowess</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="type"/>
       </param>
       <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help="">
+      <param argument="-extraction_function" type="select" optional="true" label="Function used to extract the signal" help="">
         <option value="tophat" selected="true">tophat</option>
         <option value="bartlett">bartlett</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="extraction_function"/>
       </param>
-      <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="-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">
@@ -94,13 +112,161 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_OpenSwathChromatogramExtractor"/>
-    <expand macro="manutest_OpenSwathChromatogramExtractor"/>
+  <tests><!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="extraction_function" value="tophat"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
+      </conditional>
+      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
+      <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="min_upper_edge_dist" value="0.0"/>
+      <param name="rt_window" value="-1.0"/>
+      <param name="ion_mobility_window" value="-1.0"/>
+      <param name="mz_window" value="0.05"/>
+      <param name="ppm" value="false"/>
+      <param name="is_swath" value="false"/>
+      <param name="extract_MS1" value="false"/>
+      <section name="model">
+        <param name="type" value="linear"/>
+        <param name="symmetric_regression" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathChromatogramExtractor_test_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="extraction_function" value="tophat"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
+      </conditional>
+      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
+      <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
+      <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="min_upper_edge_dist" value="0.0"/>
+      <param name="rt_window" value="50.0"/>
+      <param name="ion_mobility_window" value="-1.0"/>
+      <param name="mz_window" value="0.05"/>
+      <param name="ppm" value="false"/>
+      <param name="is_swath" value="false"/>
+      <param name="extract_MS1" value="false"/>
+      <section name="model">
+        <param name="type" value="linear"/>
+        <param name="symmetric_regression" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathChromatogramExtractor_test_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="extraction_function" value="tophat"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
+      </conditional>
+      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
+      <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="min_upper_edge_dist" value="0.0"/>
+      <param name="rt_window" value="-1.0"/>
+      <param name="ion_mobility_window" value="-1.0"/>
+      <param name="mz_window" value="0.05"/>
+      <param name="ppm" value="false"/>
+      <param name="is_swath" value="false"/>
+      <param name="extract_MS1" value="true"/>
+      <section name="model">
+        <param name="type" value="linear"/>
+        <param name="symmetric_regression" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathChromatogramExtractor_test_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="extraction_function" value="tophat"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
+      </conditional>
+      <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
+      <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="min_upper_edge_dist" value="0.0"/>
+      <param name="rt_window" value="-1.0"/>
+      <param name="ion_mobility_window" value="0.05"/>
+      <param name="mz_window" value="0.05"/>
+      <param name="ppm" value="false"/>
+      <param name="is_swath" value="true"/>
+      <param name="extract_MS1" value="false"/>
+      <section name="model">
+        <param name="type" value="linear"/>
+        <param name="symmetric_regression" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_OpenSwathChromatogramExtractor_test_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="extraction_function" value="tophat"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
+      </conditional>
+      <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
+      <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="min_upper_edge_dist" value="0.0"/>
+      <param name="rt_window" value="-1.0"/>
+      <param name="ion_mobility_window" value="-1.0"/>
+      <param name="mz_window" value="0.05"/>
+      <param name="ppm" value="false"/>
+      <param name="is_swath" value="false"/>
+      <param name="extract_MS1" value="true"/>
+      <section name="model">
+        <param name="type" value="linear"/>
+        <param name="symmetric_regression" value="false"/>
+      </section>
+      <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[Extract chromatograms (XIC) from a MS2 map file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
   <expand macro="references"/>
 </tool>