--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MaRaClusterAdapter.xml	Thu Sep 03 16:17:43 2020 +0000
@@ -0,0 +1,103 @@
+<?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: [ID Processing]-->
+<tool id="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+  <description>Facilitate input to MaRaCluster and reintegrate.</description>
+  <macros>
+    <token name="@EXECUTABLE@">MaRaClusterAdapter</token>
+    <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <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 _]) }
+#if $id_in:
+  mkdir id_in &&
+  ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
+#end if
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out &&
+#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if $id_in:
+  -id_in
+  ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
+#end if
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out
+  'out/output.${gxy2omsext("idxml")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
+
+## Postprocessing
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out/output.${gxy2omsext("idxml")}' '$out'
+#end if
+#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[{"maracluster_executable": "/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="in" argument="-in" type="data" format="mgf,mzml" multiple="true" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
+    <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="true" label="Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation" help=" select idxml data sets(s)"/>
+    <param name="pcut" argument="-pcut" type="float" optional="true" max="0.0" value="-10.0" label="log(p-value) cutoff, has to be &lt; 0.0" help="Default: -10.0"/>
+    <param name="min_cluster_size" argument="-min_cluster_size" type="integer" optional="true" min="1" value="1" label="minimum number of spectra in a cluster for consensus spectra" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
+      <param name="precursor_tolerance" argument="-precursor_tolerance" type="float" optional="true" value="20.0" label="Precursor monoisotopic mass tolerance" help=""/>
+      <param name="precursor_tolerance_units" argument="-precursor_tolerance_units" display="radio" type="select" optional="false" label="tolerance_mass_units 0=ppm, 1=Da" help="">
+        <option value="ppm" selected="true">ppm</option>
+        <option value="Da">Da</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <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="false">
+      <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests>
+    <expand macro="autotest_MaRaClusterAdapter"/>
+    <expand macro="manutest_MaRaClusterAdapter"/>
+  </tests>
+  <help><![CDATA[Facilitate input to MaRaCluster and reintegrate.
+
+
+For more information, visit http://www.openms.de/documentation/TOPP_MaRaClusterAdapter.html]]></help>
+  <expand macro="references"/>
+</tool>