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comparison TextExporter.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="TextExporter" name="TextExporter" version="2.0.0">
3 <description>Exports various XML formats to a text file.</description>
4 <macros>
5 <token name="@EXECUTABLE@">TextExporter</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>TextExporter
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_separator:
19 -separator "$param_separator"
20 #end if
21 #if $param_replacement:
22 -replacement "$param_replacement"
23 #end if
24 #if $param_quoting:
25 -quoting
26 #if " " in str($param_quoting):
27 "$param_quoting"
28 #else
29 $param_quoting
30 #end if
31 #end if
32 #if $param_no_ids:
33 -no_ids
34 #end if
35 -threads \${GALAXY_SLOTS:-24}
36 #if $param_feature_minimal:
37 -feature:minimal
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_consensus_centroids:
49 -consensus:centroids $param_consensus_centroids
50 #end if
51 #if $param_consensus_elements:
52 -consensus:elements $param_consensus_elements
53 #end if
54 #if $param_consensus_features:
55 -consensus:features $param_consensus_features
56 #end if
57 #if $param_consensus_sorting_method:
58 -consensus:sorting_method
59 #if " " in str($param_consensus_sorting_method):
60 "$param_consensus_sorting_method"
61 #else
62 $param_consensus_sorting_method
63 #end if
64 #end if
65 #if $param_consensus_sort_by_maps:
66 -consensus:sort_by_maps
67 #end if
68 #if $param_consensus_sort_by_size:
69 -consensus:sort_by_size
70 #end if
71 #if $adv_opts.adv_opts_selector=='advanced':
72 #if $adv_opts.param_force:
73 -force
74 #end if
75 #end if
76 </command>
77 <inputs>
78 <param name="param_in" type="data" format="featurexml,consensusxml,mzml,idxml" optional="False" label="Input file" help="(-in) "/>
79 <param name="param_separator" type="text" size="30" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator) ">
80 <sanitizer>
81 <valid initial="string.printable">
82 <remove value="'"/>
83 <remove value="&quot;"/>
84 </valid>
85 </sanitizer>
86 </param>
87 <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) ">
88 <sanitizer>
89 <valid initial="string.printable">
90 <remove value="'"/>
91 <remove value="&quot;"/>
92 </valid>
93 </sanitizer>
94 </param>
95 <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, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
96 <option value="none">none</option>
97 <option value="double">double</option>
98 <option value="escape">escape</option>
99 </param>
100 <param name="param_no_ids" type="boolean" truevalue="-no_ids" falsevalue="" checked="false" optional="True" label="Supresses output of identification data" help="(-no_ids) "/>
101 <param name="param_feature_minimal" 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) "/>
102 <param name="param_id_proteins_only" 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) "/>
103 <param name="param_id_peptides_only" 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) "/>
104 <param name="param_id_first_dim_rt" 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) "/>
105 <param name="param_consensus_sorting_method" type="select" optional="True" value="none" label="Sorting options can be combined" help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method">
106 <option value="none">none</option>
107 <option value="RT">RT</option>
108 <option value="MZ">MZ</option>
109 <option value="RT_then_MZ">RT_then_MZ</option>
110 <option value="intensity">intensity</option>
111 <option value="quality_decreasing">quality_decreasing</option>
112 <option value="quality_increasing">quality_increasing</option>
113 </param>
114 <param name="param_consensus_sort_by_maps" 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) "/>
115 <param name="param_consensus_sort_by_size" 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) "/>
116 <expand macro="advanced_options">
117 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
118 </expand>
119 </inputs>
120 <outputs>
121 <data name="param_out" format="tabular"/>
122 <data name="param_consensus_centroids" format="tabular"/>
123 <data name="param_consensus_elements" format="tabular"/>
124 <data name="param_consensus_features" format="tabular"/>
125 </outputs>
126 <help>**What it does**
127
128 Exports various XML formats to a text file.
129
130
131 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html</help>
132 <expand macro="references"/>
133 </tool>