diff ExternalCalibration.xml @ 10:4f6a44916c89 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

--- a/ExternalCalibration.xml	Fri May 17 10:23:33 2019 -0400
+++ b/ExternalCalibration.xml	Wed Sep 09 12:56:06 2020 +0000
@@ -1,73 +1,76 @@
 <?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: [Signal processing and preprocessing]-->
-<tool id="ExternalCalibration" name="ExternalCalibration" version="2.3.0">
+<tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Applies an external mass recalibration.</description>
   <macros>
     <token name="@EXECUTABLE@">ExternalCalibration</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[ExternalCalibration
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_offset:
-  -offset $param_offset
-#end if
-#if $param_slope:
-  -slope $param_slope
-#end if
-#if $param_power:
-  -power $param_power
-#end if
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("mzml")}'
 
-#if $rep_param_ms_level:
--ms_level
-  #for token in $rep_param_ms_level:
-    #if " " in str(token):
-      "$token.param_ms_level"
-    #else
-      $token.param_ms_level
-    #end if
-  #end for
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("mzml")}' '$out'
+#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="mzml" optional="False" label="Input peak file" help="(-in) "/>
-    <param name="param_offset" type="float" value="0.0" label="Mass offset in ppm" help="(-offset) "/>
-    <param name="param_slope" type="float" value="0.0" label="Slope (dependent on m/z)" help="(-slope) "/>
-    <param name="param_power" type="float" value="0.0" label="Power (dependent on m/z)" help="(-power) "/>
-    <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
-      <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Scans with other levels remain unchanged">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
+    <param name="offset" argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/>
+    <param name="slope" argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/>
+    <param name="power" argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/>
+    <param name="ms_level" argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_integer_valsan"/>
+    </param>
+    <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>
-    <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" format="mzml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Applies an external mass recalibration.
+  <tests>
+    <expand macro="autotest_ExternalCalibration"/>
+    <expand macro="manutest_ExternalCalibration"/>
+  </tests>
+  <help><![CDATA[Applies an external mass recalibration.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ExternalCalibration.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_ExternalCalibration.html]]></help>
+  <expand macro="references"/>
 </tool>