--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TriqlerConverter.xml	Thu Dec 01 19:22:27 2022 +0000
@@ -0,0 +1,102 @@
+<?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="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Converter to input for Triqler</description>
+  <macros>
+    <token name="@EXECUTABLE@">TriqlerConverter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir in_design &&
+ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
+mkdir out &&
+  #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
+    mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
+    #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
+    mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 
+    ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    #else
+    ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
+    #end if
+  #end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-in_design
+'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
+-out
+'out/output.${gxy2omsext("csv")}'
+  #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
+    -reannotate_filenames
+    #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
+    ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    #else
+    'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
+    #end if
+  #end if
+
+## Postprocessing
+&& mv 'out/output.${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 argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
+    <param argument="-Triqler_condition" type="text" optional="true" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
+      <expand macro="list_string_san" name="Triqler_condition"/>
+    </param>
+    <expand macro="adv_opts_macro">
+      <conditional name="reannotate_filenames_cond">
+        <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
+          <option value="no">No: process all datasets jointly</option>
+          <option value="yes">Yes: process each dataset in an independent job</option>
+        </param>
+        <when value="no">
+          <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+        </when>
+        <when value="yes">
+          <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+        </when>
+      </conditional>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
+      </param>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <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>
+  <tests/>
+  <help><![CDATA[Converter to input for Triqler
+
+
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TriqlerConverter.html]]></help>
+  <expand macro="references"/>
+</tool>