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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="TextExporter" name="TextExporter" version="1.12.0">
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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 -in ${param_in}
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13 -out ${param_out}
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14 -separator ${param_separator}
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15 -replacement ${param_replacement}
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16 -quoting ${param_quoting}
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17 ${param_no_ids}
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18 -threads \${GALAXY_SLOTS:-24}
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19 ${param_minimal}
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20 ${param_proteins_only}
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21 ${param_peptides_only}
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22 ${param_first_dim_rt}
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23 -consensus:centroids ${param_centroids}
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24 -consensus:elements ${param_elements}
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25 -consensus:features ${param_features}
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26 -consensus:sorting_method ${param_sorting_method}
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27 ${param_sort_by_maps}
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28 ${param_sort_by_size}
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29 </command>
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30 <inputs>
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31 <param name="param_in" type="data" format="featureXML,consensusXML,idXML,mzML" optional="False" label="Input file " help="(-in)"/>
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32 <param name="param_separator" type="text" size="20" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator)"/>
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33 <param name="param_replacement" type="text" size="20" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement)"/>
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34 <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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35 <option value="none">none</option>
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36 <option value="double">double</option>
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37 <option value="escape">escape</option>
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38 </param>
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39 <param name="param_no_ids" type="boolean" truevalue="-no_ids true" falsevalue="-no_ids false" checked="false" optional="True" label="Supresses output of identification data." help="(-no_ids)"/>
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40 <param name="param_minimal" type="boolean" truevalue="-feature:minimal true" falsevalue="-feature:minimal false" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity." help="(-minimal)"/>
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41 <param name="param_proteins_only" type="boolean" truevalue="-id:proteins_only true" falsevalue="-id:proteins_only false" 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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42 <param name="param_peptides_only" type="boolean" truevalue="-id:peptides_only true" falsevalue="-id:peptides_only false" 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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43 <param name="param_first_dim_rt" type="boolean" truevalue="-id:first_dim_rt true" falsevalue="-id:first_dim_rt false" 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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44 <param name="param_sorting_method" type="select" optional="True" value="none" label="Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_method" help="(-sorting_method)">
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45 <option value="none">none</option>
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46 <option value="RT">RT</option>
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47 <option value="MZ">MZ</option>
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48 <option value="RT_then_MZ">RT_then_MZ</option>
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49 <option value="intensity">intensity</option>
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50 <option value="quality_decreasing">quality_decreasing</option>
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51 <option value="quality_increasing">quality_increasing</option>
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52 </param>
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53 <param name="param_sort_by_maps" type="boolean" truevalue="-consensus:sort_by_maps true" falsevalue="-consensus:sort_by_maps false" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps)"/>
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54 <param name="param_sort_by_size" type="boolean" truevalue="-consensus:sort_by_size true" falsevalue="-consensus:sort_by_size false" 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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55 </inputs>
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56 <outputs>
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57 <data name="param_out" label="Output file (mandatory for featureXML and idXML)" format="tabular"/>
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58 <data name="param_centroids" label="Output file for centroids of consensus features" format="tabular"/>
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59 <data name="param_elements" label="Output file for elements of consensus features" format="tabular"/>
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60 <data name="param_features" label="Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing)" format="tabular"/>
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61 </outputs>
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62 <help>**What it does**
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63
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64 Exports various XML formats to a text file.
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65
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66
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67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html
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68
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69 @REFERENCES@
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70 </help>
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71 </tool>
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