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

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

--- a/FileInfo.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FileInfo.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,63 +1,73 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FileInfo" name="FileInfo" version="1.12.0">
-  <description>Shows basic information about the file, such as data ranges and file type.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FileInfo</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FileInfo
+<?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: [File Handling]-->
+  <tool id="FileInfo" name="FileInfo" version="2.0.0">
+    <description>Shows basic information about the file, such as data ranges and file type.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FileInfo</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FileInfo
 
--in ${param_in}
--in_type ${param_in_type}
--out ${param_out}
-${param_m}
-${param_p}
-${param_s}
-${param_d}
-${param_c}
-${param_v}
-${param_i}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_tsv:
+  -out_tsv $param_out_tsv
+#end if
+#if $param_m:
+  -m
+#end if
+#if $param_p:
+  -p
+#end if
+#if $param_s:
+  -s
+#end if
+#if $param_d:
+  -d
+#end if
+#if $param_c:
+  -c
+#end if
+#if $param_v:
+  -v
+#end if
+#if $param_i:
+  -i
+#end if
+-threads \${GALAXY_SLOTS:-24}
 #if $adv_opts.adv_opts_selector=='advanced':
-    -out_tsv ${adv_opts.param_out_tsv}
+    #if $adv_opts.param_force:
+  -force
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML,idXML,pepXML" optional="False" label="input file " help="(-in)"/>
-    <param name="param_in_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-in_type)">
-      <option value="mzData">mzData</option>
-      <option value="mzXML">mzXML</option>
-      <option value="mzML">mzML</option>
-      <option value="dta">dta</option>
-      <option value="dta2d">dta2d</option>
-      <option value="mgf">mgf</option>
-      <option value="featureXML">featureXML</option>
-      <option value="consensusXML">consensusXML</option>
-      <option value="idXML">idXML</option>
-      <option value="pepXML">pepXML</option>
-      <option value="fid">fid</option>
-    </param>
-    <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/>
-    <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/>
-    <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s)"/>
-    <param name="param_d" type="boolean" truevalue="-d true" falsevalue="-d false" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d)"/>
-    <param name="param_c" type="boolean" truevalue="-c true" falsevalue="-c false" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c)"/>
-    <param name="param_v" type="boolean" truevalue="-v true" falsevalue="-v false" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v)"/>
-    <param name="param_i" type="boolean" truevalue="-i true" falsevalue="-i false" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Optional output file. If left out, the output is written to the command line." format="txt"/>
-    <data name="param_out_tsv" label="Second optional output file. Tab separated flat text file." format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Shows basic information about the file, such as data ranges and file type.
+    <inputs>
+      <param format="xml,mzml,mzxml,consensusxml,txt,pepxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param checked="false" falsevalue="" help="(-m) " label="Show meta information about the whole experiment" name="param_m" optional="True" truevalue="-m" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-p) " label="Shows data processing information" name="param_p" optional="True" truevalue="-p" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-s) " label="Computes a five-number statistics of intensities, qualities, and widths" name="param_s" optional="True" truevalue="-s" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-d) " label="Show detailed listing of all spectra and chromatograms (peak files only)" name="param_d" optional="True" truevalue="-d" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-c) " label="Check for corrupt data in the file (peak files only)" name="param_c" optional="True" truevalue="-c" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-v) " label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" name="param_v" optional="True" truevalue="-v" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-i) " label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" name="param_i" optional="True" truevalue="-i" type="boolean"/>
+      <expand macro="advanced_options">
+        <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="txt" name="param_out"/>
+      <data format="tabular" name="param_out_tsv"/>
+    </outputs>
+    <help>Shows basic information about the file, such as data ranges and file type.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html</help>
+  </tool>