Mercurial > repos > galaxyp > thermo_raw_file_converter
annotate thermo_converter.xml @ 5:77a18a61aeed draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
author | galaxyp |
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date | Fri, 30 Aug 2019 10:28:22 -0400 |
parents | 344e10282449 |
children | 2d80c8b2dfc2 |
rev | line source |
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5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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1 <tool id="thermo_raw_file_converter" name="Thermo" version="1.1.10"> |
4
344e10282449
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit d570672a28e9603c044473e1278e48623a15e93e
galaxyp
parents:
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2 <description>RAW file converter</description> |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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3 <requirements> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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4 <requirement type="package" version="1.1.10">ThermoRawFileParser</requirement> |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
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5 </requirements> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
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6 <command> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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7 <![CDATA[ |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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8 #import re |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
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9 |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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10 #set $temp_stderr = "thermo_converter_stderr" |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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11 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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12 echo "" > $temp_stderr && |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
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13 |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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14 mkdir ./raws_folder && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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15 mkdir ./output_folder && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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16 #for $input_raw in $input: |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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17 #if len($input) > 1 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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18 #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw") |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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19 ln -s -f '${input_raw}' './raws_folder/${input_name}' && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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20 #else: |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
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21 ln -s -f '${input_raw}' './raws_folder/input.raw' && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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22 #end if |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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23 #end for |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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24 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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25 (ThermoRawFileParser.sh |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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26 -d=./raws_folder |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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27 -o=./output_folder |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
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28 -f=$output_format |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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29 #if $output_metadata_selector != "off": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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30 --metadata="${output_metadata_selector}" |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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31 #end if |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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32 $zlib_boolean |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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33 $peakpicking_boolean |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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34 $ignore_instrument_errors_boolean |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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35 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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36 2>> $temp_stderr) |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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37 |
2
edbeb2956484
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 9de08588cd6c525947f92bf475a144fcd6129fde
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38 && |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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39 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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40 #if len($input) == 1: |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
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41 #if $output_format == "0": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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42 mv ./output_folder/input.mgf ./output_file.out && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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43 #else if $output_format == "1": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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44 mv ./output_folder/input.mzML ./output_file.out && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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45 #else if $output_format == "2": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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46 mv ./output_folder/input.mzML ./output_file.out && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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47 #end if |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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48 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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49 #if $output_metadata_selector != "off": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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50 #if $output_metadata_selector == "0": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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51 mv ./output_folder/input-metadata.json ./input-metadata.txt && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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52 #else if $output_metadata_selector == "1": |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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53 mv ./output_folder/input-metadata.txt ./input-metadata.txt && |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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54 #end if |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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55 #end if |
2
edbeb2956484
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 9de08588cd6c525947f92bf475a144fcd6129fde
galaxyp
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56 #end if |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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57 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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58 cat $temp_stderr 2>&1; |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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59 ]]> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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60 </command> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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61 <inputs> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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62 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true" |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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63 optional="False" /> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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64 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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65 <param name="output_format" type="select" label="Output format"> |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
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66 <option value="0">mgf</option> |
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
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67 <option value="1" selected="True">mzml</option> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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68 <option value="2">Indexed mzml</option> |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
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69 </param> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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70 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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71 <param name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true" |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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72 label="Use zlib compression for the m/z ratios and intensities" help="" /> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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73 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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74 <param name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true" |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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75 label="Use the peak picking provided by the native thermo library" help="" /> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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76 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
77 <param name="ignore_instrument_errors_boolean" type="boolean" truevalue="-e" falsevalue="" checked="true" |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
78 label="Ignore missing instrument properties" help="If false, it stops the conversion if instrument properties are missing" /> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
79 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
80 <param name="output_metadata_selector" type="select" label="Output metadata" > |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
81 <option value="off" selected="True">No</option> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
82 <option value="0">json</option> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
83 <option value="1">txt</option> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
84 </param> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
85 |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
diff
changeset
|
86 </inputs> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
diff
changeset
|
87 <outputs> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
88 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
89 <!-- We use simple data outputs if we just have one file, for backwards compatibility --> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
90 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
91 <data name="output" format="mzml" from_work_dir="output_file.out" label="${tool.name} on ${on_string}"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
92 <filter>(str(input)).count(',') == 0</filter> <!-- funny way of counting the number of input files! --> |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
parents:
0
diff
changeset
|
93 <change_format> |
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
parents:
0
diff
changeset
|
94 <when input="output_format" value="0" format="mgf" /> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
95 <when input="output_format" value="2" format="txt" /> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
96 </change_format> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
97 </data> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
98 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
99 <data name="output_metadata" format="txt" label="${tool.name} on ${on_string}: Metadata" from_work_dir="input-metadata.txt"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
100 <filter>str(output_metadata_selector) != "off"</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
101 <filter>(str(input)).count(',') == 0</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
102 <change_format> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
103 <when input="output_metadata_selector" value="0" format="json" /> |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
parents:
0
diff
changeset
|
104 </change_format> |
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
parents:
0
diff
changeset
|
105 </data> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
106 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
107 <!-- We use collections if we have multiple input files --> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
108 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
109 <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
110 <filter>output_format == "0"</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
111 <filter>(str(input)).count(',') > 0</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
112 <discover_datasets pattern="(?P<designation>.+)\.mgf" directory="output_folder" ext="mgf"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
113 </collection> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
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|
114 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
115 <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
116 <filter>output_format == "1"</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
117 <filter>(str(input)).count(',') > 0</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
118 <discover_datasets pattern="(?P<designation>.+)\.mzML" ext="mzml" directory="output_folder"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
119 </collection> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
120 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
121 <collection name="output_indexedmzml_collection" type="list" label="${tool.name} on ${on_string}: Indexed mzML"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
122 <filter>output_format == "2"</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
123 <filter>(str(input)).count(',') > 0</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
124 <discover_datasets pattern="(?P<designation>.+)\.mzML" ext="mzml" directory="output_folder"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
125 </collection> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
126 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
127 <collection name="output_metadata_collection" type="list" label="${tool.name} on ${on_string}: metadata"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
128 <filter>output_metadata_selector != "off"</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
129 <filter>(str(input)).count(',') > 0</filter> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
130 <discover_datasets pattern="(?P<designation>.+)-metadata.txt" ext="txt" directory="output_folder"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
131 <discover_datasets pattern="(?P<designation>.+)-metadata.json" ext="json" directory="output_folder"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
132 </collection> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
133 |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
diff
changeset
|
134 </outputs> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
135 |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
diff
changeset
|
136 <tests> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
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|
137 <!-- Basic test --> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
138 <test expect_num_outputs="1"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
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|
139 <param name="input" value="really_small.raw"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
140 <param name="output_format" value="1"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
141 <output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" /> |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
parents:
diff
changeset
|
142 </test> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
143 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
144 <!-- Testing contents of converted mgf file with txt metadata --> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
145 <test expect_num_outputs="2"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
146 <param name="input" value="really_small.raw"/> |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
galaxyp
parents:
0
diff
changeset
|
147 <param name="output_format" value="0"/> |
5
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
148 <param name="output_metadata_selector" value="1"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
149 <output name="output"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
150 <assert_contents> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents:
4
diff
changeset
|
151 <has_text text="SCANS=36"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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152 <has_text text="RTINSECONDS=73.863181104"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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153 <has_text text="PEPMASS=675.248779296875"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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154 <has_text text="CHARGE=2+"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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155 <has_text text="121.3116455 920.2367553711"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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156 <has_text text="229.2241211 1137.6958007813"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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157 <has_text text="1577.8967285 1487.9519042969"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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158 </assert_contents> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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159 </output> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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160 <output name="output_metadata" ftype="txt"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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161 <assert_contents> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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162 <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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163 <has_text text="Instrument name=Orbitrap Fusion"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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164 <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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165 <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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166 <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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167 <has_text text="Number of scans=101"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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168 <has_text text="Scan range=1;101"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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169 <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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170 <has_text text="Time range=0.89;1.59"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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171 <has_text text="Mass range=120.0000;2000.0000"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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172 </assert_contents> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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173 </output> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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174 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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175 </test> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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176 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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177 <!-- Basic mzml collection test --> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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178 <test expect_num_outputs="1"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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179 <param name="input" value="really_small.raw,really_small_2.raw"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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180 <param name="output_format" value="1"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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181 <output_collection name="output_mzml_collection" type="list" count="2"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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182 </test> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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183 |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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184 <!-- mgf collection test with metadata --> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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185 <test expect_num_outputs="2"> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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186 <param name="input" value="really_small.raw,really_small_2.raw,really_small_3.raw"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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187 <param name="output_format" value="0"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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188 <param name="output_metadata_selector" value="0"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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189 <output_collection name="output_mgf_collection" type="list" count="3"/> |
77a18a61aeed
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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190 <output_collection name="output_metadata_collection" type="list" count="3"/> |
1
15d2a50acaeb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb
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191 </test> |
0
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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192 </tests> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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193 <help> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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194 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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195 |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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196 Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project. |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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197 |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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198 ]]> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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199 </help> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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200 <citations> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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201 <citation type="bibtex">@misc{Galaxy Proteomics Tools, |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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202 author = {Niels Hulstaert, et al.}, |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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203 title = {Galaxy Proteomics Tools}, |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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204 publisher = {GitHub}, |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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205 journal = {GitHub repository}, |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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206 year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}} |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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207 </citation> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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208 </citations> |
00c4b28150bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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209 </tool> |