diff SemanticValidator.xml @ 9:702ed84d9f4c draft

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

--- a/SemanticValidator.xml	Fri May 17 09:21:26 2019 -0400
+++ b/SemanticValidator.xml	Thu Sep 03 16:18:18 2020 +0000
@@ -1,54 +1,83 @@
 <?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="2.3.0">
+<tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <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="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[SemanticValidator
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_mapping_file:
-  -mapping_file $param_mapping_file
+## Preprocessing
+mkdir in &&
+ln -s '$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 _]) }
 #end if
--cv
-  #for token in $param_cv:
-    $token
-  #end for
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-mapping_file
+'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
+#if $cv:
+  -cv
+  ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])}
 #end if
-#end if
-&gt; $param_stdout
-]]></command>
+| tee '$stdout'
+
+## Postprocessing
+#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="analysisXML,mzml,traml,mzid,mzData,xml" optional="False" label="Input file (any xml file)" help="(-in) "/>
-    <param name="param_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="(-mapping_file) "/>
-    <param name="param_cv" type="data" format="obo" multiple="true" optional="True" size="30" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help="(-cv) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <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)"/>
+    <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>
-    <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) "/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_stdout" format="txt" label="Output from stdout"/>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>SemanticValidator for semantically validating certain XML files.
+  <tests>
+    <expand macro="autotest_SemanticValidator"/>
+    <expand macro="manutest_SemanticValidator"/>
+  </tests>
+  <help><![CDATA[SemanticValidator for semantically validating certain XML files.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SemanticValidator.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_SemanticValidator.html]]></help>
+  <expand macro="references"/>
 </tool>