diff TextExporter.xml @ 0:be5c2f82c8ef 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/TextExporter.xml	Wed Mar 01 12:52:36 2017 -0500
@@ -0,0 +1,134 @@
+<?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="TextExporter" name="TextExporter" version="2.1.0">
+  <description>Exports various XML formats to a text file.</description>
+  <macros>
+    <token name="@EXECUTABLE@">TextExporter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>TextExporter
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_separator:
+  -separator     "$param_separator"
+#end if
+#if $param_replacement:
+  -replacement     "$param_replacement"
+#end if
+#if $param_quoting:
+  -quoting $param_quoting
+#end if
+#if $param_no_ids:
+  -no_ids
+#end if
+#if $param_feature_minimal:
+  -feature:minimal
+#end if
+#if $param_feature_add_metavalues:
+  -feature:add_metavalues $param_feature_add_metavalues
+#end if
+#if $param_id_proteins_only:
+  -id:proteins_only
+#end if
+#if $param_id_peptides_only:
+  -id:peptides_only
+#end if
+#if $param_id_first_dim_rt:
+  -id:first_dim_rt
+#end if
+#if $param_id_add_metavalues:
+  -id:add_metavalues $param_id_add_metavalues
+#end if
+#if $param_id_add_hit_metavalues:
+  -id:add_hit_metavalues $param_id_add_hit_metavalues
+#end if
+#if $param_consensus_centroids:
+  -consensus:centroids $param_consensus_centroids
+#end if
+#if $param_consensus_elements:
+  -consensus:elements $param_consensus_elements
+#end if
+#if $param_consensus_features:
+  -consensus:features $param_consensus_features
+#end if
+#if $param_consensus_sorting_method:
+  -consensus:sorting_method $param_consensus_sorting_method
+#end if
+#if $param_consensus_sort_by_maps:
+  -consensus:sort_by_maps
+#end if
+#if $param_consensus_sort_by_size:
+  -consensus:sort_by_size
+#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,consensusxml,mzml,idxml" optional="False" label="Input file" help="(-in) "/>
+    <param name="param_separator" type="text" size="30" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_replacement" type="text" size="30" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_quoting" display="radio" type="select" optional="False" value="none" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
+      <option value="none" selected="true">none</option>
+      <option value="double">double</option>
+      <option value="escape">escape</option>
+    </param>
+    <param name="param_no_ids" display="radio" type="boolean" truevalue="-no_ids" falsevalue="" checked="false" optional="True" label="Suppresses output of identification data" help="(-no_ids) "/>
+    <param name="param_feature_minimal" display="radio" type="boolean" truevalue="-feature:minimal" falsevalue="" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity" help="(-minimal) "/>
+    <param name="param_feature_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/>
+    <param name="param_id_proteins_only" display="radio" type="boolean" truevalue="-id:proteins_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only) "/>
+    <param name="param_id_peptides_only" display="radio" type="boolean" truevalue="-id:peptides_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only) "/>
+    <param name="param_id_first_dim_rt" display="radio" type="boolean" truevalue="-id:first_dim_rt" falsevalue="" 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_id_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/>
+    <param name="param_id_add_hit_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_hit_metavalues) Set to -1 to omit meta values (default)"/>
+    <param name="param_consensus_sorting_method" type="select" optional="False" value="none" label="Sorting options can be combined" help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method">
+      <option value="none" selected="true">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_consensus_sort_by_maps" display="radio" type="boolean" truevalue="-consensus:sort_by_maps" falsevalue="" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps) "/>
+    <param name="param_consensus_sort_by_size" display="radio" type="boolean" truevalue="-consensus:sort_by_size" falsevalue="" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size) "/>
+    <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="tabular"/>
+    <data name="param_consensus_centroids" format="tabular"/>
+    <data name="param_consensus_elements" format="tabular"/>
+    <data name="param_consensus_features" format="tabular"/>
+  </outputs>
+  <help>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</help>
+</tool>