diff AdditiveSeries.xml @ 0:24e8f13aef7e 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/AdditiveSeries.xml	Wed Mar 01 12:49:49 2017 -0500
@@ -0,0 +1,108 @@
+<?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: [Quantitation]-->
+<tool id="AdditiveSeries" name="AdditiveSeries" version="2.1.0">
+  <description>Computes an additive series to quantify a peptide in a set of samples.</description>
+  <macros>
+    <token name="@EXECUTABLE@">AdditiveSeries</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>AdditiveSeries
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_mz_tolerance:
+  -mz_tolerance $param_mz_tolerance
+#end if
+#if $param_rt_tolerance:
+  -rt_tolerance $param_rt_tolerance
+#end if
+
+#if $rep_param_concentrations:
+-concentrations
+  #for token in $rep_param_concentrations:
+    #if " " in str(token):
+      "$token.param_concentrations"
+    #else
+      $token.param_concentrations
+    #end if
+  #end for
+#end if
+#if $param_feature_rt:
+  -feature_rt $param_feature_rt
+#end if
+#if $param_feature_mz:
+  -feature_mz $param_feature_mz
+#end if
+#if $param_standard_rt:
+  -standard_rt $param_standard_rt
+#end if
+#if $param_standard_mz:
+  -standard_mz $param_standard_mz
+#end if
+#if $param_plot_write_gnuplot_output:
+  -plot:write_gnuplot_output
+#end if
+#if $param_plot_out_gp:
+  -plot:out_gp     "$param_plot_out_gp"
+#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="featurexml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance) "/>
+    <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance) "/>
+    <repeat name="rep_param_concentrations" min="1" max="1" title="param_concentrations">
+      <param name="param_concentrations" type="text" size="30" value="0" label="List of spiked concentrations" help="(-concentrations) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt) "/>
+    <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz) "/>
+    <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt) "/>
+    <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz) "/>
+    <param name="param_plot_write_gnuplot_output" display="radio" type="boolean" truevalue="-plot:write_gnuplot_output" falsevalue="" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output) "/>
+    <param name="param_plot_out_gp" type="text" size="30" label="base file name (3 files with different extensions are created)" help="(-out_gp) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <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="xml"/>
+  </outputs>
+  <help>Computes an additive series to quantify a peptide in a set of samples.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help>
+</tool>