diff OpenSwathFeatureXMLToTSV.xml @ 8:b8192a9b7f9c draft

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

--- a/OpenSwathFeatureXMLToTSV.xml	Fri May 17 10:25:02 2019 -0400
+++ b/OpenSwathFeatureXMLToTSV.xml	Wed Sep 09 13:01:10 2020 +0000
@@ -1,67 +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: [Targeted Experiments]-->
-<tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.3.0">
+<tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Converts a featureXML to a mProphet tsv.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</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[OpenSwathFeatureXMLToTSV
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
+## Preprocessing
+mkdir in &&
+${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir tr &&
+ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-  #for token in $param_in:
-    $token
-  #end for
-#if $param_tr:
-  -tr $param_tr
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_short_format:
-  -short_format
-#end if
-#if $param_best_scoring_peptide:
-  -best_scoring_peptide     "$param_best_scoring_peptide"
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+-tr
+'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
+-out
+'out/output.${gxy2omsext("csv")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("csv")}' '$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="featurexml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
+    <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="TraML transition file" help=" select traml data sets(s)"/>
+    <param name="short_format" argument="-short_format" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write short (one peptide per line) or long format (one transition per line)" help=""/>
+    <param name="best_scoring_peptide" argument="-best_scoring_peptide" type="text" optional="true" value="" label="If only the best scoring feature per peptide should be printed, give the variable name" help="">
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_tr" type="data" format="traml" optional="False" label="TraML transition file" help="(-tr) "/>
-    <param name="param_short_format" display="radio" type="boolean" truevalue="-short_format" falsevalue="" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)" help="(-short_format) "/>
-    <param name="param_best_scoring_peptide" type="text" size="30" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <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_out" format="tabular"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Converts a featureXML to a mProphet tsv.
+  <tests>
+    <expand macro="autotest_OpenSwathFeatureXMLToTSV"/>
+    <expand macro="manutest_OpenSwathFeatureXMLToTSV"/>
+  </tests>
+  <help><![CDATA[Converts a featureXML to a mProphet tsv.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
+  <expand macro="references"/>
 </tool>