Mercurial > repos > galaxyp > openms_mzmlsplitter

annotate MzMLSplitter.xml @ 7:ab079a6757c1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
author galaxyp
date Fri, 17 May 2019 10:22:12 -0400
parents b14efb4cf1ea
children a2bf6f5def91
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MzMLSplitter" name="MzMLSplitter" version="2.3.0">
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5 <description>Splits an mzML file into multiple parts</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MzMLSplitter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="aggressive"><![CDATA[
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13 mkdir parts/ &&
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15 MzMLSplitter
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17 #if $param_in:
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18 -in $param_in
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19 #end if
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20 #if $param_out:
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21 -out "parts/$param_out"
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22 #else
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23 -out "parts/MzML"
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24 #end if
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25 #if $param_parts:
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26 -parts $param_parts
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27 #end if
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28 #if $param_size:
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29 -size $param_size
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30 #end if
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31 #if $param_unit:
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32 -unit
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33 #if " " in str($param_unit):
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34 "$param_unit"
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35 #else
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36 $param_unit
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37 #end if
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38 #end if
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39 #if $param_no_chrom:
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40 -no_chrom
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41 #end if
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42 #if $param_no_spec:
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43 -no_spec
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44 #end if
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45 #if $adv_opts.adv_opts_selector=='advanced':
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46 #if $adv_opts.param_force:
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47 -force
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48 #end if
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49 #end if
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50 -threads "\${GALAXY_SLOTS:-1}"
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51 ]]></command>
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52 <inputs>
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53 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
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54 <param name="param_out" type="text" size="30" label="Prefix for output files ('_part1of2.mzML' etc" help="(-out) will be appended; default: same as 'in' without the file extension)">
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55 <sanitizer>
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56 <valid initial="string.printable">
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57 <remove value="'"/>
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58 <remove value="&quot;"/>
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59 </valid>
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60 </sanitizer>
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61 </param>
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62 <param name="param_parts" type="integer" min="1" optional="True" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help="(-parts) "/>
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63 <param name="param_size" type="integer" min="0" optional="True" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help="(-size) "/>
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64 <param name="param_unit" display="radio" type="select" optional="False" value="MB" label="Unit for 'size' (base 1024)" help="(-unit) ">
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65 <option value="KB">KB</option>
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66 <option value="MB" selected="true">MB</option>
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67 <option value="GB">GB</option>
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68 </param>
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69 <param name="param_no_chrom" display="radio" type="boolean" truevalue="-no_chrom" falsevalue="" checked="false" optional="True" label="Remove chromatograms, keep only spectra" help="(-no_chrom) "/>
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70 <param name="param_no_spec" display="radio" type="boolean" truevalue="-no_spec" falsevalue="" checked="false" optional="True" label="Remove spectra, keep only chromatograms" help="(-no_spec) "/>
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71 <expand macro="advanced_options">
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72 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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73 </expand>
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74 </inputs>
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75 <outputs>
6
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76 <collection name="parts" type="list">
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77 <discover_datasets pattern="__name_and_ext__" format="mzml" directory="parts" />
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78 </collection>
0
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79 </outputs>
6
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80 <tests>
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81 <test>
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82 <param name="param_in" value="FileFilter_1_input.mzML"/>
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83 <param name="param_parts" value="2" />
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84 <output_collection name="parts" type="list">
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85 <element name="MzML_part1of2" file="MzMLSplitter_output_part1.mzML" ftype="mzml" />
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86 <element name="MzML_part2of2" file="MzMLSplitter_output_part2.mzML" ftype="mzml" />
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87 </output_collection>
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88 </test>
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89 </tests>
0
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90 <help>Splits an mzML file into multiple parts
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91
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92
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93 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MzMLSplitter.html</help>
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94 <expand macro="references"/>
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95 </tool>