diff QCExporter.xml @ 13:b36a5233eda9 draft

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

--- a/QCExporter.xml	Wed May 15 06:43:56 2019 -0400
+++ b/QCExporter.xml	Thu Aug 27 23:15:51 2020 +0000
@@ -1,65 +1,79 @@
 <?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="QCExporter" name="QCExporter" version="2.3.0">
+<tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Will extract several qp from several run/sets in a tabular format.</description>
   <macros>
     <token name="@EXECUTABLE@">QCExporter</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
-  <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[QCExporter
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir mapping &&
+ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
+mkdir out_csv &&
+
+## Main program call
 
-#if $rep_param_names:
--names
-  #for token in $rep_param_names:
-    #if " " in str(token):
-      "$token.param_names"
-    #else
-      $token.param_names
-    #end if
-  #end for
-#end if
-#if $param_mapping:
-  -mapping $param_mapping
-#end if
-#if $param_out_csv:
-  -out_csv $param_out_csv
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-mapping
+'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)'
+-out_csv
+'out_csv/output.${gxy2omsext("csv")}'
+
+## Postprocessing
+&& mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
+#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="qcml" optional="False" label="Input qcml file" help="(-in) "/>
-    <repeat name="rep_param_names" min="0" title="param_names">
-      <param name="param_names" type="text" size="30" label="The name of the target runs or sets to be exported from" help="(-names) If empty, from all will be exported">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
+    <param name="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param name="names" argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_string_val"/>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="mapping" argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv 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>
-    </repeat>
-    <param name="param_mapping" type="data" format="tabular" optional="False" label="The mapping of the exported table's headers to the according qp cvs" help="(-mapping) The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported"/>
-    <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>
+    <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>
   </inputs>
   <outputs>
-    <data name="param_out_csv" format="tabular"/>
+    <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Will extract several qp from several run/sets in a tabular format.
+  <tests>
+    <expand macro="autotest_QCExporter"/>
+    <expand macro="manutest_QCExporter"/>
+  </tests>
+  <help><![CDATA[Will extract several qp from several run/sets in a tabular format.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCExporter.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_QCExporter.html]]></help>
+  <expand macro="references"/>
 </tool>