--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMetaboIdent.xml	Wed Sep 09 19:59:38 2020 +0000
@@ -0,0 +1,162 @@
+<?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="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+  <description>Detects features in MS1 data based on metabolite identifications.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</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 &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir id &&
+ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+mkdir out &&
+#if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir lib_out &&
+#end if
+#if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir chrom_out &&
+#end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir candidates_out &&
+#end if
+#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir trafo_out &&
+#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-id
+'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
+-out
+'out/output.${gxy2omsext("featurexml")}'
+#if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -lib_out
+  'lib_out/output.${gxy2omsext("traml")}'
+#end if
+#if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -chrom_out
+  'chrom_out/output.${gxy2omsext("mzml")}'
+#end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -candidates_out
+  'candidates_out/output.${gxy2omsext("featurexml")}'
+#end if
+#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -trafo_out
+  'trafo_out/output.${gxy2omsext("trafoxml")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("featurexml")}' '$out'
+#if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
+#end if
+#if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
+#end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
+#end if
+#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
+    <param name="id" argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
+    <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
+      <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
+      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each assay" help=""/>
+      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a compound" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
+      <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If zero, calculated based on 'detect:peak_width'"/>
+    </section>
+    <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
+      <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="5.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
+      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
+      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
+    </section>
+    <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
+      <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of elution model to fit to features" help="">
+        <option value="symmetric" selected="true">symmetric</option>
+        <option value="asymmetric">asymmetric</option>
+        <option value="none">none</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
+      <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
+      <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
+      <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
+        <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
+        <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
+        <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help=""/>
+        <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help=""/>
+      </section>
+    </section>
+    <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="lib_out_FLAG">lib_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
+      <option value="chrom_out_FLAG">chrom_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
+      <option value="candidates_out_FLAG">candidates_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
+      <option value="trafo_out_FLAG">trafo_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
+    <data name="lib_out" label="${tool.name} on ${on_string}: lib_out" format="traml">
+      <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
+      <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
+      <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
+      <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${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_FeatureFinderMetaboIdent"/>
+    <expand macro="manutest_FeatureFinderMetaboIdent"/>
+  </tests>
+  <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
+
+
+For more information, visit http://www.openms.de/documentation/UTILS_FeatureFinderMetaboIdent.html]]></help>
+  <expand macro="references"/>
+</tool>