diff SemanticValidator.xml @ 13:ff9d0d1c2c1c draft

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

--- a/SemanticValidator.xml	Fri Nov 06 20:13:35 2020 +0000
+++ b/SemanticValidator.xml	Thu Dec 01 18:57:56 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: [Utilities]-->
-<tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>SemanticValidator for semantically validating certain XML files.</description>
   <macros>
     <token name="@EXECUTABLE@">SemanticValidator</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -20,9 +18,14 @@
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir mapping_file &&
 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
-#if $cv:
-  mkdir cv &&
-  ${ ' '.join(["ln -s '%s' 'cv/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _]) }
+#if $cv_cond.cv:
+  mkdir cv_cond.cv &&
+  #if $cv_cond.cv_select == "no"
+  mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} && 
+  ${' '.join(["ln -s '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])}
+  #else
+  ln -s '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' &&
+  #end if
 #end if
 
 ## Main program call
@@ -35,9 +38,13 @@
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 -mapping_file
 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
-#if $cv:
+#if $cv_cond.cv:
   -cv
-  ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])}
+  #if $cv_cond.cv_select == "no"
+  ${' '.join(["'cv_cond.cv/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])}
+  #else
+  'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)'
+  #end if
 #end if
 | tee '$stdout'
 
@@ -50,13 +57,24 @@
     <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="mzdata,mzid,mzml,traml,xml" optional="false" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/>
-    <param name="mapping_file" argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/>
-    <param name="cv" argument="-cv" type="data" format="obo" multiple="true" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
+    <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" optional="false" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/>
+    <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/>
+    <conditional name="cv_cond">
+      <param name="cv_select" type="select" label="Run tool in batch mode for -cv">
+        <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="-cv" type="data" format="obo" multiple="true" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-cv" type="data" format="obo" multiple="false" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
+      </when>
+    </conditional>
     <expand macro="adv_opts_macro">
-      <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">
@@ -71,13 +89,18 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SemanticValidator"/>
-    <expand macro="manutest_SemanticValidator"/>
-  </tests>
+  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+    <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
+    <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
+       <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents>
+    </output>
+  </test>
+</tests>
   <help><![CDATA[SemanticValidator for semantically validating certain XML files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SemanticValidator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SemanticValidator.html]]></help>
   <expand macro="references"/>
 </tool>