diff ERPairFinder.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

--- a/ERPairFinder.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/ERPairFinder.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,51 +1,73 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="ERPairFinder" name="ERPairFinder" version="1.12.0">
-  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
-  <macros>
-    <token name="@EXECUTABLE@">ERPairFinder</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>ERPairFinder
+<?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: [Utilities]-->
+  <tool id="ERPairFinder" name="ERPairFinder" version="2.0.0">
+    <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
+    <macros>
+      <token name="@EXECUTABLE@">ERPairFinder</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>ERPairFinder
 
--in ${param_in}
--pair_in ${param_pair_in}
--out ${param_out}
--feature_out ${param_feature_out}
--precursor_mass_tolerance ${param_precursor_mass_tolerance}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_pair_in:
+  -pair_in $param_pair_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_feature_out:
+  -feature_out $param_feature_out
+#end if
+#if $param_precursor_mass_tolerance:
+  -precursor_mass_tolerance $param_precursor_mass_tolerance
+#end if
+-threads \${GALAXY_SLOTS:-24}
 #if $adv_opts.adv_opts_selector=='advanced':
-    -RT_tolerance ${adv_opts.param_RT_tolerance}
-    -max_charge ${adv_opts.param_max_charge}
-    -intensity_threshold ${adv_opts.param_intensity_threshold}
-    -max_isotope ${adv_opts.param_max_isotope}
-    -expansion_range ${adv_opts.param_expansion_range}
+    #if $adv_opts.param_RT_tolerance:
+  -RT_tolerance $adv_opts.param_RT_tolerance
+#end if
+    #if $adv_opts.param_max_charge:
+  -max_charge $adv_opts.param_max_charge
+#end if
+    #if $adv_opts.param_intensity_threshold:
+  -intensity_threshold $adv_opts.param_intensity_threshold
+#end if
+    #if $adv_opts.param_max_isotope:
+  -max_isotope $adv_opts.param_max_isotope
+#end if
+    #if $adv_opts.param_expansion_range:
+  -expansion_range $adv_opts.param_expansion_range
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file containing the ER spectra." help="(-in)"/>
-    <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in)"/>
-    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features." help="(-precursor_mass_tolerance)"/>
-    <expand macro="advanced_options">
-      <param name="param_RT_tolerance" type="float" min="1.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help="(-RT_tolerance)"/>
-      <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search for." help="(-max_charge)"/>
-      <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation." help="(-intensity_threshold)"/>
-      <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope)"/>
-      <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th." help="(-expansion_range)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output consensusXML file were the pairs of the feature are written into." format="consensusXML"/>
-    <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/>
-  </outputs>
-  <help>**What it does**
-
-Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
+    <inputs>
+      <param format="mzml" help="(-in) " label="Input mzML file containing the ER spectra" name="param_in" optional="False" type="data"/>
+      <param format="txt" help="(-pair_in) " label="Pair-file in the format: m/z-light m/z-heavy charge rt" name="param_pair_in" optional="False" type="data"/>
+      <param help="(-precursor_mass_tolerance) " label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" min="0.0" name="param_precursor_mass_tolerance" optional="True" type="float" value="0.3"/>
+      <expand macro="advanced_options">
+        <param help="(-RT_tolerance) " label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" min="1.0" name="param_RT_tolerance" optional="True" type="float" value="200.0"/>
+        <param help="(-max_charge) " label="Maximal charge state features should be search fo" min="1" name="param_max_charge" optional="True" type="integer" value="3"/>
+        <param help="(-intensity_threshold) " label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" min="-1.0" name="param_intensity_threshold" optional="True" type="float" value="-1.0"/>
+        <param help="(-max_isotope) " label="Max isotope of the isotope distribution to be considered" min="2" name="param_max_isotope" optional="True" type="integer" value="3"/>
+        <param help="(-expansion_range) " label="The range that is used to extend the isotope distribution with null intensity peaks in Th" min="0.0" name="param_expansion_range" optional="True" type="float" value="5.0"/>
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="consensusxml" name="param_out"/>
+      <data format="xml" name="param_feature_out"/>
+    </outputs>
+    <help>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html</help>
+  </tool>