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