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annotate TextExporter.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="TextExporter" name="TextExporter" version="2.0.0">
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5 <description>Exports various XML formats to a text file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">TextExporter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>TextExporter
0
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14
4
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_separator:
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22 -separator &quot;$param_separator&quot;
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23 #end if
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24 #if $param_replacement:
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25 -replacement &quot;$param_replacement&quot;
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26 #end if
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27 #if $param_quoting:
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28 -quoting
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29 #if &quot; &quot; in str($param_quoting):
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30 &quot;$param_quoting&quot;
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31 #else
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32 $param_quoting
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33 #end if
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34 #end if
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35 #if $param_no_ids:
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36 -no_ids
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37 #end if
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38 -threads \${GALAXY_SLOTS:-24}
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39 #if $param_feature_minimal:
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40 -feature:minimal
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41 #end if
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42 #if $param_feature_add_metavalues:
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43 -feature:add_metavalues $param_feature_add_metavalues
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44 #end if
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45 #if $param_id_proteins_only:
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46 -id:proteins_only
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47 #end if
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48 #if $param_id_peptides_only:
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49 -id:peptides_only
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50 #end if
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51 #if $param_id_first_dim_rt:
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52 -id:first_dim_rt
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53 #end if
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54 #if $param_consensus_centroids:
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55 -consensus:centroids $param_consensus_centroids
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56 #end if
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57 #if $param_consensus_elements:
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58 -consensus:elements $param_consensus_elements
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59 #end if
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60 #if $param_consensus_features:
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61 -consensus:features $param_consensus_features
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62 #end if
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63 #if $param_consensus_sorting_method:
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64 -consensus:sorting_method
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65 #if &quot; &quot; in str($param_consensus_sorting_method):
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66 &quot;$param_consensus_sorting_method&quot;
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67 #else
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68 $param_consensus_sorting_method
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69 #end if
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70 #end if
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71 #if $param_consensus_sort_by_maps:
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72 -consensus:sort_by_maps
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73 #end if
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74 #if $param_consensus_sort_by_size:
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75 -consensus:sort_by_size
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76 #end if
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77 #if $adv_opts.adv_opts_selector=='advanced':
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78 #if $adv_opts.param_force:
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79 -force
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80 #end if
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81 #end if
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82 </command>
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83 <inputs>
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84 <param format="xml,consensusxml,mzml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
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85 <param help="(-separator) " label="The used separator character(s); if not set the 'tab' character is used" name="param_separator" size="30" type="text">
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86 <sanitizer>
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87 <valid initial="string.printable">
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88 <remove value="'"/>
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89 <remove value="&quot;"/>
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90 </valid>
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91 </sanitizer>
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92 </param>
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93 <param help="(-replacement) " label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" name="param_replacement" size="30" type="text" value="_">
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94 <sanitizer>
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95 <valid initial="string.printable">
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96 <remove value="'"/>
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97 <remove value="&quot;"/>
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98 </valid>
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99 </sanitizer>
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100 </param>
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101 <param help="(-quoting) " 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" name="param_quoting" optional="True" type="select" value="none">
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102 <option value="none">none</option>
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103 <option value="double">double</option>
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104 <option value="escape">escape</option>
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105 </param>
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106 <param checked="false" falsevalue="" help="(-no_ids) " label="Suppresses output of identification data" name="param_no_ids" optional="True" truevalue="-no_ids" type="boolean"/>
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107 <param checked="false" falsevalue="" help="(-minimal) " label="Set this flag to write only three attributes: RT, m/z, and intensity" name="param_feature_minimal" optional="True" truevalue="-feature:minimal" type="boolean"/>
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108 <param help="(-add_metavalues) Set to -1 to omit meta values (default)" label="Add columns for meta values which occur with a certain frequency (0-100%)" max="100" min="-1" name="param_feature_add_metavalues" optional="True" type="integer" value="-1"/>
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109 <param checked="false" falsevalue="" help="(-proteins_only) " label="Set this flag if you want only protein information from an idXML file" name="param_id_proteins_only" optional="True" truevalue="-id:proteins_only" type="boolean"/>
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110 <param checked="false" falsevalue="" help="(-peptides_only) " label="Set this flag if you want only peptide information from an idXML file" name="param_id_peptides_only" optional="True" truevalue="-id:peptides_only" type="boolean"/>
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111 <param checked="false" falsevalue="" help="(-first_dim_rt) " label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" name="param_id_first_dim_rt" optional="True" truevalue="-id:first_dim_rt" type="boolean"/>
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112 <param help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method" label="Sorting options can be combined" name="param_consensus_sorting_method" optional="True" type="select" value="none">
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113 <option value="none">none</option>
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114 <option value="RT">RT</option>
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115 <option value="MZ">MZ</option>
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116 <option value="RT_then_MZ">RT_then_MZ</option>
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117 <option value="intensity">intensity</option>
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118 <option value="quality_decreasing">quality_decreasing</option>
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119 <option value="quality_increasing">quality_increasing</option>
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120 </param>
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121 <param checked="false" falsevalue="" help="(-sort_by_maps) " label="Apply a stable sort by the covered maps, lexicographically" name="param_consensus_sort_by_maps" optional="True" truevalue="-consensus:sort_by_maps" type="boolean"/>
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122 <param checked="false" falsevalue="" help="(-sort_by_size) " label="Apply a stable sort by decreasing size (i.e., the number of elements)" name="param_consensus_sort_by_size" optional="True" truevalue="-consensus:sort_by_size" type="boolean"/>
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123 <expand macro="advanced_options">
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124 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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125 </expand>
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126 </inputs>
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127 <outputs>
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128 <data format="tabular" name="param_out"/>
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129 <data format="tabular" name="param_consensus_centroids"/>
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130 <data format="tabular" name="param_consensus_elements"/>
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131 <data format="tabular" name="param_consensus_features"/>
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132 </outputs>
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133 <help>Exports various XML formats to a text file.
0
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134
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135
4
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136 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html</help>
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137 </tool>