diff TextExporter.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TextExporter.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,71 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="TextExporter" name="TextExporter" version="1.12.0">
+  <description>Exports various XML formats to a text file.</description>
+  <macros>
+    <token name="@EXECUTABLE@">TextExporter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>TextExporter
+
+-in ${param_in}
+-out ${param_out}
+-separator ${param_separator}
+-replacement ${param_replacement}
+-quoting ${param_quoting}
+${param_no_ids}
+-threads \${GALAXY_SLOTS:-24} 
+${param_minimal}
+${param_proteins_only}
+${param_peptides_only}
+${param_first_dim_rt}
+-consensus:centroids ${param_centroids}
+-consensus:elements ${param_elements}
+-consensus:features ${param_features}
+-consensus:sorting_method ${param_sorting_method}
+${param_sort_by_maps}
+${param_sort_by_size}
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="featureXML,consensusXML,idXML,mzML" optional="False" label="Input file " help="(-in)"/>
+    <param name="param_separator" type="text" size="20" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator)"/>
+    <param name="param_replacement" type="text" size="20" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement)"/>
+    <param name="param_quoting" type="select" optional="True" value="none" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting)">
+      <option value="none">none</option>
+      <option value="double">double</option>
+      <option value="escape">escape</option>
+    </param>
+    <param name="param_no_ids" type="boolean" truevalue="-no_ids true" falsevalue="-no_ids false" checked="false" optional="True" label="Supresses output of identification data." help="(-no_ids)"/>
+    <param name="param_minimal" type="boolean" truevalue="-feature:minimal true" falsevalue="-feature:minimal false" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity." help="(-minimal)"/>
+    <param name="param_proteins_only" type="boolean" truevalue="-id:proteins_only true" falsevalue="-id:proteins_only false" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only)"/>
+    <param name="param_peptides_only" type="boolean" truevalue="-id:peptides_only true" falsevalue="-id:peptides_only false" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only)"/>
+    <param name="param_first_dim_rt" type="boolean" truevalue="-id:first_dim_rt true" falsevalue="-id:first_dim_rt false" checked="false" optional="True" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)." help="(-first_dim_rt)"/>
+    <param name="param_sorting_method" type="select" optional="True" value="none" label="Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_method" help="(-sorting_method)">
+      <option value="none">none</option>
+      <option value="RT">RT</option>
+      <option value="MZ">MZ</option>
+      <option value="RT_then_MZ">RT_then_MZ</option>
+      <option value="intensity">intensity</option>
+      <option value="quality_decreasing">quality_decreasing</option>
+      <option value="quality_increasing">quality_increasing</option>
+    </param>
+    <param name="param_sort_by_maps" type="boolean" truevalue="-consensus:sort_by_maps true" falsevalue="-consensus:sort_by_maps false" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps)"/>
+    <param name="param_sort_by_size" type="boolean" truevalue="-consensus:sort_by_size true" falsevalue="-consensus:sort_by_size false" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file (mandatory for featureXML and idXML)" format="tabular"/>
+    <data name="param_centroids" label="Output file for centroids of consensus features" format="tabular"/>
+    <data name="param_elements" label="Output file for elements of consensus features" format="tabular"/>
+    <data name="param_features" label="Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing)" format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+Exports various XML formats to a text file.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html
+
+@REFERENCES@
+</help>
+</tool>