Mercurial > repos > galaxyp > thermo_raw_file_converter

annotate thermo_converter.xml @ 4:9381e3a3a1a6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit d570672a28e9603c044473e1278e48623a15e93e
author galaxyp
date Fri, 26 Apr 2019 14:32:39 -0400
parents 756817e04abe
children a3263ea5abb2
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1 <tool id="thermo_raw_file_converter" name="Thermo" version="1.1.2">
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2 <description>RAW file converter</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2">ThermoRawFileParser</requirement>
0
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8
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9 ln -s '$input' ./input.raw &&
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11 ThermoRawFileParser.sh
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12 -i=input.raw
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13 -o=./
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14 -f=$output_format
0
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15 #if $metadata:
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16 --metadata=1
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17 #end if
2
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18 &&
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19 #if $output_format == '0':
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20 mv ./input.mgf '$output'
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21 #else:
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22 mv ./input.mzML '$output'
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23 #end if
0
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" />
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28 <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False"
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29 label="Output metadata" help="" />
1
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30 <param name="output_format" type="select" label="Choose an output format">
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31 <option value="0">mgf</option>
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32 <option value="1" selected="True">mzml</option>
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33 </param>
0
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34 </inputs>
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35 <outputs>
1
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36 <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}">
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37 <change_format>
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38 <when input="output_format" value="0" format="mgf" />
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39 </change_format>
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40 </data>
0
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41 <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata">
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42 <filter>metadata</filter>
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43 </data>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input" value="fake_input.txt"/>
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48 <assert_command>
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49 <has_text text="ThermoRawFileParser.sh"/>
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50 </assert_command>
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51 </test>
1
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52 <test>
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53 <param name="input" value="fake_input.txt"/>
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54 <param name="output_format" value="0"/>
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55 <assert_command>
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56 <has_text text="-f=0"/>
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57 </assert_command>
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58 </test>
0
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59 </tests>
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60 <help>
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61 <![CDATA[
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62
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63 Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project.
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64
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65 ]]>
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66 </help>
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67 <citations>
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68 <citation type="bibtex">@misc{Galaxy Proteomics Tools,
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69 author = {Niels Hulstaert, et al.},
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70 title = {Galaxy Proteomics Tools},
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71 publisher = {GitHub},
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72 journal = {GitHub repository},
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73 year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}}
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74 </citation>
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75 </citations>
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76 </tool>