Mercurial > repos > galaxyp > openms_tmtanalyzer
annotate TMTAnalyzer.xml @ 3:a415db0d29f5 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
| author | galaxyp |
|---|---|
| date | Thu, 27 Apr 2017 13:13:31 -0400 |
| parents | 0bf790828adc |
| children |
| rev | line source |
|---|---|
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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1 <?xml version='1.0' encoding='UTF-8'?> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTD2Galaxy.--> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Quantitation]--> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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4 <tool id="TMTAnalyzer" name="TMTAnalyzer" version="2.1.0"> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Calculates TMT quantitative values for peptides</description> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">TMTAnalyzer</token> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 <expand macro="references"/> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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12 <expand macro="requirements"/> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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13 <command>TMTAnalyzer |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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14 |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 #if $param_in: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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16 -in $param_in |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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17 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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18 #if $param_out: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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19 -out $param_out |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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20 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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21 #if $param_out_mzq: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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22 -out_mzq $param_out_mzq |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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23 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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24 #if $param_out_stats: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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25 -out_stats $param_out_stats |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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26 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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27 #if $param_id_pool: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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28 -id_pool "$param_id_pool" |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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29 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 #if $param_algorithm_Extraction_select_activation: |
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2
0bf790828adc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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31 -algorithm:Extraction:select_activation |
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0bf790828adc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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32 #if " " in str($param_algorithm_Extraction_select_activation): |
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0bf790828adc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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33 "$param_algorithm_Extraction_select_activation" |
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0bf790828adc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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34 #else |
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0bf790828adc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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35 $param_algorithm_Extraction_select_activation |
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0bf790828adc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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36 #end if |
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0
78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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37 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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38 #if $param_algorithm_Extraction_reporter_mass_shift: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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39 -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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41 |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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42 #if $rep_param_algorithm_Extraction_channel_active: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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43 -algorithm:Extraction:channel_active |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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44 #for token in $rep_param_algorithm_Extraction_channel_active: |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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45 #if " " in str(token): |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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46 "$token.param_algorithm_Extraction_channel_active" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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47 #else |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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48 $token.param_algorithm_Extraction_channel_active |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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49 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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50 #end for |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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51 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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52 #if $param_algorithm_Quantification_channel_reference: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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53 -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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54 #end if |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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55 #if $adv_opts.adv_opts_selector=='advanced': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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56 #if $adv_opts.param_force: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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57 -force |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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58 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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59 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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60 #if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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61 -algorithm:Quantification:isotope_correction:tmt-6plex |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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62 #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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63 #if " " in str(token): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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64 "$token.param_algorithm_Quantification_isotope_correction_tmt_6plex" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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65 #else |
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66 $token.param_algorithm_Quantification_isotope_correction_tmt_6plex |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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67 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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68 #end for |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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69 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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70 #if $adv_opts.param_algorithm_Quantification_do_normalization: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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71 -algorithm:Quantification:do_normalization |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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72 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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73 #if $adv_opts.param_algorithm_MetaInformation_Program: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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74 -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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75 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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76 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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77 </command> |
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78fc5d6d54ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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78 <inputs> |
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79 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/> |
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80 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)"> |
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81 <sanitizer> |
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82 <valid initial="string.printable"> |
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83 <remove value="'"/> |
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84 <remove value="""/> |
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85 </valid> |
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86 </sanitizer> |
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87 </param> |
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88 <param name="param_algorithm_Extraction_select_activation" type="select" optional="False" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" help="(-select_activation) Set to empty string if you want to disable filtering"> |
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89 <option value="Collision-induced dissociation">Collision-induced dissociation</option> |
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90 <option value="Post-source decay">Post-source decay</option> |
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91 <option value="Plasma desorption">Plasma desorption</option> |
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92 <option value="Surface-induced dissociation">Surface-induced dissociation</option> |
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93 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> |
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94 <option value="Electron capture dissociation">Electron capture dissociation</option> |
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95 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> |
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96 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> |
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97 <option value="High-energy collision-induced dissociation" selected="true">High-energy collision-induced dissociation</option> |
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98 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
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99 <option value="Photodissociation">Photodissociation</option> |
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100 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
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101 <option value=""></option> |
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102 </param> |
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103 <param name="param_algorithm_Extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/> |
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104 <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active"> |
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105 <param name="param_algorithm_Extraction_channel_active" type="text" size="30" value="126:liver 131:lung" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format <channel>:<name>," help="(-channel_active) e.g. "114:myref","115:liver""> |
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106 <sanitizer> |
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107 <valid initial="string.printable"> |
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108 <remove value="'"/> |
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109 <remove value="""/> |
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110 </valid> |
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111 </sanitizer> |
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112 </param> |
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113 </repeat> |
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114 <param name="param_algorithm_Quantification_channel_reference" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-channel_reference) "/> |
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115 <expand macro="advanced_options"> |
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116 <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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117 <repeat name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_tmt_6plex"> |
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118 <param name="param_algorithm_Quantification_isotope_correction_tmt_6plex" type="text" size="30" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0" label="Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'"> |
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119 <sanitizer> |
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120 <valid initial="string.printable"> |
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121 <remove value="'"/> |
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122 <remove value="""/> |
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123 </valid> |
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124 </sanitizer> |
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125 </param> |
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126 </repeat> |
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127 <param name="param_algorithm_Quantification_do_normalization" display="radio" type="boolean" truevalue="-algorithm:Quantification:do_normalization" falsevalue="" checked="false" optional="True" label="Normalize channels?" help="(-do_normalization) Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/> |
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128 <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::TMTAnalyzer" label="" help="(-Program) "> |
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129 <sanitizer> |
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130 <valid initial="string.printable"> |
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131 <remove value="'"/> |
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132 <remove value="""/> |
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133 </valid> |
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134 </sanitizer> |
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135 </param> |
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136 </expand> |
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137 </inputs> |
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138 <outputs> |
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139 <data name="param_out" format="consensusxml"/> |
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140 <data name="param_out_mzq" format="mzq"/> |
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141 <data name="param_out_stats" format="tabular"/> |
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142 </outputs> |
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143 <help>Calculates TMT quantitative values for peptides |
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144 |
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145 |
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146 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help> |
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147 </tool> |