diff IDRTCalibration.xml @ 0:0f901d73c008 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDRTCalibration.xml	Wed Mar 01 12:38:59 2017 -0500
@@ -0,0 +1,56 @@
+<?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: [ID Processing]-->
+<tool id="IDRTCalibration" name="IDRTCalibration" version="2.1.0">
+  <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDRTCalibration</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDRTCalibration
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_calibrant_1_reference:
+  -calibrant_1_reference $param_calibrant_1_reference
+#end if
+#if $param_calibrant_2_reference:
+  -calibrant_2_reference $param_calibrant_2_reference
+#end if
+#if $param_calibrant_1_input:
+  -calibrant_1_input $param_calibrant_1_input
+#end if
+#if $param_calibrant_2_input:
+  -calibrant_2_input $param_calibrant_2_input
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
+    <param name="param_calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help="(-calibrant_1_reference) "/>
+    <param name="param_calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help="(-calibrant_2_reference) "/>
+    <param name="param_calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file" help="(-calibrant_1_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/>
+    <param name="param_calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file" help="(-calibrant_2_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/>
+    <expand macro="advanced_options">
+      <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="idxml"/>
+  </outputs>
+  <help>Can be used to calibrate RTs of peptide hits linearly to standards.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html</help>
+</tool>