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comparison TextExporter.xml @ 0:be5c2f82c8ef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:52:36 -0500
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children d06df685f78c
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-1:000000000000 0:be5c2f82c8ef
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="TextExporter" name="TextExporter" version="2.1.0">
5 <description>Exports various XML formats to a text file.</description>
6 <macros>
7 <token name="@EXECUTABLE@">TextExporter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>TextExporter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_separator:
22 -separator "$param_separator"
23 #end if
24 #if $param_replacement:
25 -replacement "$param_replacement"
26 #end if
27 #if $param_quoting:
28 -quoting $param_quoting
29 #end if
30 #if $param_no_ids:
31 -no_ids
32 #end if
33 #if $param_feature_minimal:
34 -feature:minimal
35 #end if
36 #if $param_feature_add_metavalues:
37 -feature:add_metavalues $param_feature_add_metavalues
38 #end if
39 #if $param_id_proteins_only:
40 -id:proteins_only
41 #end if
42 #if $param_id_peptides_only:
43 -id:peptides_only
44 #end if
45 #if $param_id_first_dim_rt:
46 -id:first_dim_rt
47 #end if
48 #if $param_id_add_metavalues:
49 -id:add_metavalues $param_id_add_metavalues
50 #end if
51 #if $param_id_add_hit_metavalues:
52 -id:add_hit_metavalues $param_id_add_hit_metavalues
53 #end if
54 #if $param_consensus_centroids:
55 -consensus:centroids $param_consensus_centroids
56 #end if
57 #if $param_consensus_elements:
58 -consensus:elements $param_consensus_elements
59 #end if
60 #if $param_consensus_features:
61 -consensus:features $param_consensus_features
62 #end if
63 #if $param_consensus_sorting_method:
64 -consensus:sorting_method $param_consensus_sorting_method
65 #end if
66 #if $param_consensus_sort_by_maps:
67 -consensus:sort_by_maps
68 #end if
69 #if $param_consensus_sort_by_size:
70 -consensus:sort_by_size
71 #end if
72 #if $adv_opts.adv_opts_selector=='advanced':
73 #if $adv_opts.param_force:
74 -force
75 #end if
76 #end if
77 </command>
78 <inputs>
79 <param name="param_in" type="data" format="featurexml,consensusxml,mzml,idxml" optional="False" label="Input file" help="(-in) "/>
80 <param name="param_separator" type="text" size="30" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator) ">
81 <sanitizer>
82 <valid initial="string.printable">
83 <remove value="'"/>
84 <remove value="&quot;"/>
85 </valid>
86 </sanitizer>
87 </param>
88 <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) ">
89 <sanitizer>
90 <valid initial="string.printable">
91 <remove value="'"/>
92 <remove value="&quot;"/>
93 </valid>
94 </sanitizer>
95 </param>
96 <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) ">
97 <option value="none" selected="true">none</option>
98 <option value="double">double</option>
99 <option value="escape">escape</option>
100 </param>
101 <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) "/>
102 <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) "/>
103 <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)"/>
104 <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) "/>
105 <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) "/>
106 <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) "/>
107 <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)"/>
108 <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)"/>
109 <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">
110 <option value="none" selected="true">none</option>
111 <option value="RT">RT</option>
112 <option value="MZ">MZ</option>
113 <option value="RT_then_MZ">RT_then_MZ</option>
114 <option value="intensity">intensity</option>
115 <option value="quality_decreasing">quality_decreasing</option>
116 <option value="quality_increasing">quality_increasing</option>
117 </param>
118 <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) "/>
119 <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) "/>
120 <expand macro="advanced_options">
121 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
122 </expand>
123 </inputs>
124 <outputs>
125 <data name="param_out" format="tabular"/>
126 <data name="param_consensus_centroids" format="tabular"/>
127 <data name="param_consensus_elements" format="tabular"/>
128 <data name="param_consensus_features" format="tabular"/>
129 </outputs>
130 <help>Exports various XML formats to a text file.
131
132
133 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html</help>
134 </tool>