diff FileConverter.xml @ 0:2ef180905190 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/FileConverter.xml	Wed Mar 01 12:46:54 2017 -0500
@@ -0,0 +1,84 @@
+<?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="FileConverter" name="FileConverter" version="2.1.0">
+  <description>Converts between different MS file formats.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FileConverter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FileConverter
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_UID_postprocessing:
+  -UID_postprocessing $param_UID_postprocessing
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_type:
+  -out_type
+  #if " " in str($param_out_type):
+    "$param_out_type"
+  #else
+    $param_out_type
+  #end if
+#end if
+#if $param_write_mzML_index:
+  -write_mzML_index
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_TIC_DTA2D:
+  -TIC_DTA2D
+#end if
+    #if $adv_opts.param_MGF_compact:
+  -MGF_compact
+#end if
+    #if $adv_opts.param_process_lowmemory:
+  -process_lowmemory
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
+    <param name="param_UID_postprocessing" display="radio" type="select" optional="False" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs">
+      <option value="none">none</option>
+      <option value="ensure" selected="true">ensure</option>
+      <option value="reassign">reassign</option>
+    </param>
+    <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
+      <option value="mzData">mzData</option>
+      <option value="mzXML">mzXML</option>
+      <option value="mzML">mzML</option>
+      <option value="cachedMzML">cachedMzML</option>
+      <option value="dta2d">dta2d</option>
+      <option value="mgf">mgf</option>
+      <option value="featureXML">featureXML</option>
+      <option value="consensusXML">consensusXML</option>
+      <option value="edta">edta</option>
+      <option value="csv">csv</option>
+    </param>
+    <param name="param_write_mzML_index" display="radio" type="boolean" truevalue="-write_mzML_index" falsevalue="" checked="false" optional="True" label="Add an index to the file when writing mzML files (default: no index)" help="(-write_mzML_index) "/>
+    <expand macro="advanced_options">
+      <param name="param_TIC_DTA2D" display="radio" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help="(-TIC_DTA2D) "/>
+      <param name="param_MGF_compact" display="radio" type="boolean" truevalue="-MGF_compact" falsevalue="" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact) "/>
+      <param name="param_process_lowmemory" display="radio" type="boolean" truevalue="-process_lowmemory" falsevalue="" checked="false" optional="True" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms"/>
+      <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" metadata_source="param_in" auto_format="true"/>
+  </outputs>
+  <help>Converts between different MS file formats.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
+</tool>