Mercurial > repos > galaxyp > thermo_raw_file_converter
comparison thermo_converter.xml @ 1:15d2a50acaeb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
author | galaxyp |
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date | Fri, 21 Sep 2018 18:49:31 -0400 |
parents | 00c4b28150bd |
children | edbeb2956484 |
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0:00c4b28150bd | 1:15d2a50acaeb |
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9 ln -s '$input' ./input.raw && | 9 ln -s '$input' ./input.raw && |
10 | 10 |
11 ThermoRawFileParser.sh | 11 ThermoRawFileParser.sh |
12 -i=input.raw | 12 -i=input.raw |
13 -o=./ | 13 -o=./ |
14 -f=1 | 14 -f=$output_format |
15 #if $metadata: | 15 #if $metadata: |
16 --metadata=1 | 16 --metadata=1 |
17 #end if | 17 #end if |
18 ]]> | 18 ]]> |
19 </command> | 19 </command> |
20 <inputs> | 20 <inputs> |
21 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" /> | 21 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" /> |
22 <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False" | 22 <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False" |
23 label="Output metadata" help="" /> | 23 label="Output metadata" help="" /> |
24 <param name="output_format" type="select" label="Choose an output format"> | |
25 <option value="0">mgf</option> | |
26 <option value="1" selected="True">mzml</option> | |
27 </param> | |
24 </inputs> | 28 </inputs> |
25 <outputs> | 29 <outputs> |
26 <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}" /> | 30 <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}"> |
31 <change_format> | |
32 <when input="output_format" value="0" format="mgf" /> | |
33 </change_format> | |
34 </data> | |
27 <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata"> | 35 <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata"> |
28 <filter>metadata</filter> | 36 <filter>metadata</filter> |
29 </data> | 37 </data> |
30 </outputs> | 38 </outputs> |
31 <tests> | 39 <tests> |
32 <test> | 40 <test> |
33 <param name="input" value="fake_input.txt"/> | 41 <param name="input" value="fake_input.txt"/> |
34 <assert_command> | 42 <assert_command> |
35 <has_text text="ThermoRawFileParser.sh"/> | 43 <has_text text="ThermoRawFileParser.sh"/> |
44 </assert_command> | |
45 </test> | |
46 <test> | |
47 <param name="input" value="fake_input.txt"/> | |
48 <param name="output_format" value="0"/> | |
49 <assert_command> | |
50 <has_text text="-f=0"/> | |
36 </assert_command> | 51 </assert_command> |
37 </test> | 52 </test> |
38 </tests> | 53 </tests> |
39 <help> | 54 <help> |
40 <![CDATA[ | 55 <![CDATA[ |