--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ClusterMassTracesByPrecursor.xml	Thu Aug 27 19:37:26 2020 -0400
@@ -0,0 +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: [Utilities]-->
+<tool id="ClusterMassTracesByPrecursor" name="ClusterMassTracesByPrecursor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+  <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.</description>
+  <macros>
+    <token name="@EXECUTABLE@">ClusterMassTracesByPrecursor</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_ms1 &&
+ln -s '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' &&
+mkdir in_swath &&
+ln -s '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in_ms1
+'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)'
+-in_swath
+'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)'
+-out
+'out/output.${gxy2omsext("mzml")}'
+
+## 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="in_ms1" argument="-in_ms1" type="data" format="consensusxml" optional="false" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
+    <param name="in_swath" argument="-in_swath" type="data" format="consensusxml" optional="false" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
+    <param name="assign_unassigned_to_all" argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/>
+    <param name="min_pearson_correlation" argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
+    <param name="max_lag" argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
+    <param name="min_nr_ions" argument="-min_nr_ions" type="integer" optional="true" value="3" label="Minimal number of ions to report a spectrum" help=""/>
+    <param name="max_rt_apex_difference" argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
+    <param name="swath_lower" argument="-swath_lower" type="float" optional="true" value="0.0" label="Swath lower isolation window" help=""/>
+    <param name="swath_upper" argument="-swath_upper" type="float" optional="true" value="0.0" label="Swath upper isolation window" help=""/>
+    <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="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>
+  <tests>
+    <expand macro="autotest_ClusterMassTracesByPrecursor"/>
+    <expand macro="manutest_ClusterMassTracesByPrecursor"/>
+  </tests>
+  <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.]]></help>
+  <expand macro="references"/>
+</tool>