diff FuzzyDiff.xml @ 0:d309f10848f8 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/FuzzyDiff.xml	Wed Mar 01 12:39:44 2017 -0500
@@ -0,0 +1,104 @@
+<?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="FuzzyDiff" name="FuzzyDiff" version="2.1.0">
+  <description>Compares two files, tolerating numeric differences.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FuzzyDiff</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FuzzyDiff
+
+#if $param_in1:
+  -in1 $param_in1
+#end if
+#if $param_in2:
+  -in2 $param_in2
+#end if
+#if $param_ratio:
+  -ratio $param_ratio
+#end if
+#if $param_absdiff:
+  -absdiff $param_absdiff
+#end if
+#if $param_verbose:
+  -verbose $param_verbose
+#end if
+#if $param_tab_width:
+  -tab_width $param_tab_width
+#end if
+#if $param_first_column:
+  -first_column $param_first_column
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    
+#if $rep_param_whitelist:
+-whitelist
+  #for token in $rep_param_whitelist:
+    #if " " in str(token):
+      "$token.param_whitelist"
+    #else
+      $token.param_whitelist
+    #end if
+  #end for
+#end if
+    
+#if $rep_param_matched_whitelist:
+-matched_whitelist
+  #for token in $rep_param_matched_whitelist:
+    #if " " in str(token):
+      "$token.param_matched_whitelist"
+    #else
+      $token.param_matched_whitelist
+    #end if
+  #end for
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+&gt; $param_stdout
+</command>
+  <inputs>
+    <param name="param_in1" type="data" format="text" label="first input file" help="(-in1) "/>
+    <param name="param_in2" type="data" format="text" label="second input file" help="(-in2) "/>
+    <param name="param_ratio" type="float" min="1.0" optional="True" value="1.0" label="acceptable relative erro" help="(-ratio) Only one of 'ratio' or 'absdiff' has to be satisfied.  Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
+    <param name="param_absdiff" type="float" min="0.0" optional="True" value="0.0" label="acceptable absolute difference" help="(-absdiff) Only one of 'ratio' or 'absdiff' has to be satisfied. "/>
+    <param name="param_verbose" type="integer" min="0" max="3" optional="True" value="2" label="set verbose level: &lt;br&gt;0 = very quiet mode (absolutely no output) &lt;br&gt;1 = quiet mode (no output unless differences detected) &lt;br&gt;2 = default (include summary at end) &lt;br&gt;3 = continue after errors" help="(-verbose) "/>
+    <param name="param_tab_width" type="integer" min="1" optional="True" value="8" label="tabulator width, used for calculation of column numbers" help="(-tab_width) "/>
+    <param name="param_first_column" type="integer" min="0" optional="True" value="1" label="number of first column, used for calculation of column numbers" help="(-first_column) "/>
+    <expand macro="advanced_options">
+      <repeat name="rep_param_whitelist" min="0" max="1" title="param_whitelist">
+        <param name="param_whitelist" type="text" size="30" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help="(-whitelist) ">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <repeat name="rep_param_matched_whitelist" min="0" max="1" title="param_matched_whitelist">
+        <param name="param_matched_whitelist" type="text" size="30" label="Lines where one file contains one string and the other file another string are skipped. Input is given as list of colon separated tuples," help="(-matched_whitelist) e.g. String1:String2 String3:String4">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <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_stdout" format="text" label="Output from stdout"/>
+  </outputs>
+  <help>Compares two files, tolerating numeric differences.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FuzzyDiff.html</help>
+</tool>