--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathAssayGenerator.xml	Wed Mar 01 12:22:47 2017 -0500
@@ -0,0 +1,134 @@
+<?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 CTD2Galaxy.-->
+<!--Proposed Tool Section: [Targeted Experiments]-->
+<tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="2.1.0">
+  <description>Generates assays according to different models for a specific TraML</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathAssayGenerator
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_min_transitions:
+  -min_transitions $param_min_transitions
+#end if
+#if $param_max_transitions:
+  -max_transitions $param_max_transitions
+#end if
+#if $param_allowed_fragment_types:
+  -allowed_fragment_types     "$param_allowed_fragment_types"
+#end if
+#if $param_allowed_fragment_charges:
+  -allowed_fragment_charges     "$param_allowed_fragment_charges"
+#end if
+#if $param_enable_detection_specific_losses:
+  -enable_detection_specific_losses
+#end if
+#if $param_enable_detection_unspecific_losses:
+  -enable_detection_unspecific_losses
+#end if
+#if $param_enable_identification_specific_losses:
+  -enable_identification_specific_losses
+#end if
+#if $param_enable_identification_unspecific_losses:
+  -enable_identification_unspecific_losses
+#end if
+#if $param_enable_identification_ms2_precursors:
+  -enable_identification_ms2_precursors
+#end if
+#if $param_enable_ms1_uis_scoring:
+  -enable_ms1_uis_scoring
+#end if
+#if $param_enable_ms2_uis_scoring:
+  -enable_ms2_uis_scoring
+#end if
+#if $param_max_num_alternative_localizations:
+  -max_num_alternative_localizations $param_max_num_alternative_localizations
+#end if
+#if $param_enable_reannotation:
+  -enable_reannotation
+#end if
+#if $param_precursor_mz_threshold:
+  -precursor_mz_threshold $param_precursor_mz_threshold
+#end if
+#if $param_precursor_lower_mz_limit:
+  -precursor_lower_mz_limit $param_precursor_lower_mz_limit
+#end if
+#if $param_precursor_upper_mz_limit:
+  -precursor_upper_mz_limit $param_precursor_upper_mz_limit
+#end if
+#if $param_product_mz_threshold:
+  -product_mz_threshold $param_product_mz_threshold
+#end if
+#if $param_product_lower_mz_limit:
+  -product_lower_mz_limit $param_product_lower_mz_limit
+#end if
+#if $param_product_upper_mz_limit:
+  -product_upper_mz_limit $param_product_upper_mz_limit
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_swath_windows_file:
+  -swath_windows_file $adv_opts.param_swath_windows_file
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
+    <param name="param_min_transitions" type="integer" value="6" label="minimal number of transitions" help="(-min_transitions) "/>
+    <param name="param_max_transitions" type="integer" value="6" label="maximal number of transitions" help="(-max_transitions) "/>
+    <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_enable_detection_specific_losses" display="radio" type="boolean" truevalue="-enable_detection_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help="(-enable_detection_specific_losses) "/>
+    <param name="param_enable_detection_unspecific_losses" display="radio" type="boolean" truevalue="-enable_detection_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help="(-enable_detection_unspecific_losses) "/>
+    <param name="param_enable_identification_specific_losses" display="radio" type="boolean" truevalue="-enable_identification_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for identification fragment ions should be allowed" help="(-enable_identification_specific_losses) "/>
+    <param name="param_enable_identification_unspecific_losses" display="radio" type="boolean" truevalue="-enable_identification_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help="(-enable_identification_unspecific_losses) "/>
+    <param name="param_enable_identification_ms2_precursors" display="radio" type="boolean" truevalue="-enable_identification_ms2_precursors" falsevalue="" checked="false" optional="True" label="set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level)" help="(-enable_identification_ms2_precursors) This may help in identification if the MS1 signal is weak"/>
+    <param name="param_enable_ms1_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms1_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS1-UIS assays for UIS scoring should be generated" help="(-enable_ms1_uis_scoring) "/>
+    <param name="param_enable_ms2_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms2_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS2-UIS assays for UIS scoring should be generated" help="(-enable_ms2_uis_scoring) "/>
+    <param name="param_max_num_alternative_localizations" type="integer" value="20" label="maximum number of site-localization permutations" help="(-max_num_alternative_localizations) "/>
+    <param name="param_enable_reannotation" display="radio" type="boolean" truevalue="-enable_reannotation" falsevalue="" checked="false" optional="True" label="set this flag if reannotation of fragment ions should be allowed" help="(-enable_reannotation) "/>
+    <param name="param_precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help="(-precursor_mz_threshold) "/>
+    <param name="param_precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help="(-precursor_lower_mz_limit) "/>
+    <param name="param_precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help="(-precursor_upper_mz_limit) "/>
+    <param name="param_product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help="(-product_mz_threshold) "/>
+    <param name="param_product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help="(-product_lower_mz_limit) "/>
+    <param name="param_product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help="(-product_upper_mz_limit) "/>
+    <expand macro="advanced_options">
+      <param name="param_swath_windows_file" type="data" format="txt" optional="True" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
+      <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="traml"/>
+  </outputs>
+  <help>Generates assays according to different models for a specific TraML
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAssayGenerator.html</help>
+</tool>