diff OpenSwathRewriteToFeatureXML.xml @ 9:175016416031 draft

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

--- a/OpenSwathRewriteToFeatureXML.xml	Fri May 17 09:59:17 2019 -0400
+++ b/OpenSwathRewriteToFeatureXML.xml	Wed Sep 09 20:13:11 2020 +0000
@@ -1,48 +1,80 @@
 <?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="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.3.0">
+<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</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[OpenSwathRewriteToFeatureXML
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_csv:
-  -csv $param_csv
+## Preprocessing
+#if $csv:
+  mkdir csv &&
+  ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
 #end if
-#if $param_featureXML:
-  -featureXML $param_featureXML
-#end if
-#if $param_out:
-  -out $param_out
+mkdir featureXML &&
+ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+#if $csv:
+  -csv
+  'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)'
 #end if
-#if $param_FDR_cutoff:
-  -FDR_cutoff $param_FDR_cutoff
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+-featureXML
+'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)'
+-out
+'out/output.${gxy2omsext("featurexml")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("featurexml")}' '$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_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/>
-    <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
-    <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
-    <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) "/>
+    <param name="csv" argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
+    <param name="featureXML" argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/>
+    <param name="FDR_cutoff" argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
+    <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>
   </inputs>
   <outputs>
-    <data name="param_out" format="featurexml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.
+  <tests>
+    <expand macro="autotest_OpenSwathRewriteToFeatureXML"/>
+    <expand macro="manutest_OpenSwathRewriteToFeatureXML"/>
+  </tests>
+  <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathRewriteToFeatureXML.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathRewriteToFeatureXML.html]]></help>
+  <expand macro="references"/>
 </tool>