Mercurial > repos > galaxyp > openms_filefilter
annotate FileFilter.xml @ 8:4b5c7feac8db draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author | galaxyp |
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date | Tue, 20 Mar 2018 14:29:29 -0400 |
parents | fce0d752c6c5 |
children | 348aec6301b1 |
rev | line source |
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0
fa19593551c6
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'?> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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3 <!--Proposed Tool Section: [File Handling]--> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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4 <tool id="FileFilter" name="FileFilter" version="2.3.0"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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6 <macros> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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7 <token name="@EXECUTABLE@">FileFilter</token> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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8 <import>macros.xml</import> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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9 </macros> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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10 <expand macro="references"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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11 <expand macro="stdio"/> |
fa19593551c6
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"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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13 <command>FileFilter |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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14 |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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15 #if $param_in: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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16 -in $param_in |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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17 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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18 #if $param_out: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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19 -out $param_out |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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20 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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21 #if $param_out_type: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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22 -out_type |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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23 #if " " in str($param_out_type): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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24 "$param_out_type" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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25 #else |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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26 $param_out_type |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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27 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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28 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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29 #if $param_rt: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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30 -rt "$param_rt" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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31 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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32 #if $param_mz: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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33 -mz "$param_mz" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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34 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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35 #if $param_int: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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36 -int "$param_int" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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37 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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38 #if $param_sort: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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39 -sort |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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40 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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41 #if $param_peak_options_sn: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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42 -peak_options:sn $param_peak_options_sn |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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43 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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44 |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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45 #if $rep_param_peak_options_rm_pc_charge: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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46 -peak_options:rm_pc_charge |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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47 #for token in $rep_param_peak_options_rm_pc_charge: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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48 #if " " in str(token): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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49 "$token.param_peak_options_rm_pc_charge" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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50 #else |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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51 $token.param_peak_options_rm_pc_charge |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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52 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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53 #end for |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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54 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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55 #if $param_peak_options_pc_mz_range: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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56 -peak_options:pc_mz_range "$param_peak_options_pc_mz_range" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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57 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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58 |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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59 #if $rep_param_peak_options_pc_mz_list: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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60 -peak_options:pc_mz_list |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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61 #for token in $rep_param_peak_options_pc_mz_list: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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62 #if " " in str(token): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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63 "$token.param_peak_options_pc_mz_list" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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64 #else |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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65 $token.param_peak_options_pc_mz_list |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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66 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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67 #end for |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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68 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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69 |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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70 #if $rep_param_peak_options_level: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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71 -peak_options:level |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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72 #for token in $rep_param_peak_options_level: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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73 #if " " in str(token): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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74 "$token.param_peak_options_level" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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75 #else |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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76 $token.param_peak_options_level |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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77 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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78 #end for |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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79 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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80 #if $param_peak_options_sort_peaks: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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81 -peak_options:sort_peaks |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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82 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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83 #if $param_peak_options_no_chromatograms: |
fa19593551c6
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84 -peak_options:no_chromatograms |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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85 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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86 #if $param_peak_options_remove_chromatograms: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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87 -peak_options:remove_chromatograms |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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88 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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89 #if $param_peak_options_mz_precision: |
1
020fc2600133
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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90 -peak_options:mz_precision |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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91 #if " " in str($param_peak_options_mz_precision): |
020fc2600133
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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92 "$param_peak_options_mz_precision" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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93 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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94 $param_peak_options_mz_precision |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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95 #end if |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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96 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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97 #if $param_peak_options_int_precision: |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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98 -peak_options:int_precision |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
galaxyp
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99 #if " " in str($param_peak_options_int_precision): |
020fc2600133
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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100 "$param_peak_options_int_precision" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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101 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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102 $param_peak_options_int_precision |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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103 #end if |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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104 #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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105 #if $param_peak_options_indexed_file: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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106 -peak_options:indexed_file |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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107 #end if |
3
59adb20eb08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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108 #if $param_peak_options_zlib_compression: |
59adb20eb08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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109 -peak_options:zlib_compression |
59adb20eb08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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110 #end if |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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111 #if $param_peak_options_numpress_masstime: |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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112 -peak_options:numpress:masstime |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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113 #if " " in str($param_peak_options_numpress_masstime): |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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114 "$param_peak_options_numpress_masstime" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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115 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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116 $param_peak_options_numpress_masstime |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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117 #end if |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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118 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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119 #if $param_peak_options_numpress_masstime_error: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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120 -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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121 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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122 #if $param_peak_options_numpress_intensity: |
1
020fc2600133
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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123 -peak_options:numpress:intensity |
020fc2600133
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
galaxyp
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124 #if " " in str($param_peak_options_numpress_intensity): |
020fc2600133
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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125 "$param_peak_options_numpress_intensity" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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126 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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127 $param_peak_options_numpress_intensity |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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128 #end if |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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129 #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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130 #if $param_peak_options_numpress_intensity_error: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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131 -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error |
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132 #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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133 #if $param_spectra_remove_zoom: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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134 -spectra:remove_zoom |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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135 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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136 #if $param_spectra_remove_mode: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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137 -spectra:remove_mode |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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138 #if " " in str($param_spectra_remove_mode): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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139 "$param_spectra_remove_mode" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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140 #else |
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141 $param_spectra_remove_mode |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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142 #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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143 #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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144 #if $param_spectra_remove_activation: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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145 -spectra:remove_activation |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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146 #if " " in str($param_spectra_remove_activation): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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147 "$param_spectra_remove_activation" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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148 #else |
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149 $param_spectra_remove_activation |
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150 #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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151 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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152 #if $param_spectra_remove_collision_energy: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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153 -spectra:remove_collision_energy "$param_spectra_remove_collision_energy" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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154 #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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155 #if $param_spectra_remove_isolation_window_width: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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156 -spectra:remove_isolation_window_width "$param_spectra_remove_isolation_window_width" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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157 #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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158 #if $param_spectra_select_zoom: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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159 -spectra:select_zoom |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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160 #end if |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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161 #if $param_spectra_select_mode: |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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162 -spectra:select_mode |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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163 #if " " in str($param_spectra_select_mode): |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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164 "$param_spectra_select_mode" |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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165 #else |
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166 $param_spectra_select_mode |
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167 #end if |
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168 #end if |
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169 #if $param_spectra_select_activation: |
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170 -spectra:select_activation |
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171 #if " " in str($param_spectra_select_activation): |
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172 "$param_spectra_select_activation" |
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173 #else |
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174 $param_spectra_select_activation |
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175 #end if |
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176 #end if |
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177 #if $param_spectra_select_collision_energy: |
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178 -spectra:select_collision_energy "$param_spectra_select_collision_energy" |
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179 #end if |
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180 #if $param_spectra_select_isolation_window_width: |
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181 -spectra:select_isolation_window_width "$param_spectra_select_isolation_window_width" |
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182 #end if |
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183 #if $param_spectra_select_polarity: |
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184 -spectra:select_polarity |
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185 #if " " in str($param_spectra_select_polarity): |
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186 "$param_spectra_select_polarity" |
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187 #else |
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188 $param_spectra_select_polarity |
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189 #end if |
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190 #end if |
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191 #if $param_feature_q: |
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192 -feature:q "$param_feature_q" |
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193 #end if |
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194 |
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195 #if $rep_param_consensus_map: |
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196 -consensus:map |
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197 #for token in $rep_param_consensus_map: |
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198 #if " " in str(token): |
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199 "$token.param_consensus_map" |
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200 #else |
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201 $token.param_consensus_map |
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202 #end if |
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203 #end for |
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204 #end if |
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205 #if $param_consensus_map_and: |
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206 -consensus:map_and |
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207 #end if |
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208 #if $param_consensus_blackorwhitelist_blacklist: |
1
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209 -consensus:blackorwhitelist:blacklist |
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210 #if " " in str($param_consensus_blackorwhitelist_blacklist): |
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211 "$param_consensus_blackorwhitelist_blacklist" |
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212 #else |
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213 $param_consensus_blackorwhitelist_blacklist |
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214 #end if |
0
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215 #end if |
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216 #if $param_consensus_blackorwhitelist_file: |
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217 -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file |
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218 #end if |
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219 |
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220 #if $rep_param_consensus_blackorwhitelist_maps: |
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221 -consensus:blackorwhitelist:maps |
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222 #for token in $rep_param_consensus_blackorwhitelist_maps: |
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223 #if " " in str(token): |
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224 "$token.param_consensus_blackorwhitelist_maps" |
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225 #else |
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226 $token.param_consensus_blackorwhitelist_maps |
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227 #end if |
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228 #end for |
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229 #end if |
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230 #if $param_consensus_blackorwhitelist_rt: |
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231 -consensus:blackorwhitelist:rt $param_consensus_blackorwhitelist_rt |
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232 #end if |
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233 #if $param_consensus_blackorwhitelist_mz: |
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234 -consensus:blackorwhitelist:mz $param_consensus_blackorwhitelist_mz |
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235 #end if |
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236 #if $param_consensus_blackorwhitelist_use_ppm_tolerance: |
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237 -consensus:blackorwhitelist:use_ppm_tolerance |
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238 #end if |
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239 #if $param_f_and_c_charge: |
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240 -f_and_c:charge "$param_f_and_c_charge" |
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241 #end if |
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242 #if $param_f_and_c_size: |
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243 -f_and_c:size "$param_f_and_c_size" |
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244 #end if |
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245 |
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246 #if $rep_param_f_and_c_remove_meta: |
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247 -f_and_c:remove_meta |
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248 #for token in $rep_param_f_and_c_remove_meta: |
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249 #if " " in str(token): |
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250 "$token.param_f_and_c_remove_meta" |
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251 #else |
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252 $token.param_f_and_c_remove_meta |
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253 #end if |
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254 #end for |
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255 #end if |
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256 #if $param_id_keep_best_score_id: |
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257 -id:keep_best_score_id |
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258 #end if |
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259 |
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260 #if $rep_param_id_sequences_whitelist: |
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261 -id:sequences_whitelist |
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262 #for token in $rep_param_id_sequences_whitelist: |
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263 #if " " in str(token): |
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264 "$token.param_id_sequences_whitelist" |
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265 #else |
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266 $token.param_id_sequences_whitelist |
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267 #end if |
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268 #end for |
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269 #end if |
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270 |
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271 #if $rep_param_id_accessions_whitelist: |
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272 -id:accessions_whitelist |
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273 #for token in $rep_param_id_accessions_whitelist: |
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274 #if " " in str(token): |
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275 "$token.param_id_accessions_whitelist" |
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276 #else |
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277 $token.param_id_accessions_whitelist |
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278 #end if |
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279 #end for |
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280 #end if |
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281 #if $param_id_remove_annotated_features: |
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282 -id:remove_annotated_features |
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283 #end if |
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284 #if $param_id_remove_unannotated_features: |
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285 -id:remove_unannotated_features |
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286 #end if |
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287 #if $param_id_remove_unassigned_ids: |
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288 -id:remove_unassigned_ids |
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289 #end if |
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290 #if $param_id_blacklist: |
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291 -id:blacklist $param_id_blacklist |
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292 #end if |
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293 #if $param_id_rt: |
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294 -id:rt $param_id_rt |
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295 #end if |
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296 #if $param_id_mz: |
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297 -id:mz $param_id_mz |
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298 #end if |
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299 #if $param_id_blacklist_imperfect: |
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300 -id:blacklist_imperfect |
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301 #end if |
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302 #if $param_algorithm_SignalToNoise_win_len: |
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303 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len |
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304 #end if |
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305 #if $param_algorithm_SignalToNoise_bin_count: |
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306 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count |
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307 #end if |
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308 #if $param_algorithm_SignalToNoise_min_required_elements: |
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309 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements |
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310 #end if |
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311 #if $param_algorithm_SignalToNoise_write_log_messages: |
1
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312 -algorithm:SignalToNoise:write_log_messages |
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313 #if " " in str($param_algorithm_SignalToNoise_write_log_messages): |
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314 "$param_algorithm_SignalToNoise_write_log_messages" |
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315 #else |
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316 $param_algorithm_SignalToNoise_write_log_messages |
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317 #end if |
0
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318 #end if |
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319 #if $adv_opts.adv_opts_selector=='advanced': |
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320 #if $adv_opts.param_force: |
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321 -force |
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322 #end if |
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323 #if $adv_opts.param_id_remove_clashes: |
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324 -id:remove_clashes |
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325 #end if |
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326 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: |
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327 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity |
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328 #end if |
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329 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: |
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330 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor |
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331 #end if |
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332 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: |
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333 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile |
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334 #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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335 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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336 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode |
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337 #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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338 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: |
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339 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window |
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340 #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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341 #end if |
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342 </command> |
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343 <inputs> |
3
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344 <param name="param_in" type="data" format="mzml,featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/> |
0
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345 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type) "> |
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346 <option value="mzML">mzML</option> |
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347 <option value="featureXML">featureXML</option> |
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348 <option value="consensusXML">consensusXML</option> |
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349 </param> |
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350 <param name="param_rt" type="text" size="30" value=":" label="Retention time range to extract" help="(-rt) "> |
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351 <sanitizer> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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352 <valid initial="string.printable"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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353 <remove value="'"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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354 <remove value="""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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355 </valid> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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356 </sanitizer> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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357 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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358 <param name="param_mz" type="text" size="30" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="(-mz) "> |
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359 <sanitizer> |
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360 <valid initial="string.printable"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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361 <remove value="'"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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362 <remove value="""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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363 </valid> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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364 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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365 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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366 <param name="param_int" type="text" size="30" value=":" label="Intensity range to extract" help="(-int) "> |
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367 <sanitizer> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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368 <valid initial="string.printable"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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369 <remove value="'"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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370 <remove value="""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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371 </valid> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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372 </sanitizer> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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373 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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374 <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/> |
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375 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N > 'sn' values only" help="(-sn) "/> |
7
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3
diff
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376 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" title="param_peak_options_rm_pc_charge"> |
0
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377 <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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378 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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379 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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380 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
381 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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382 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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383 </sanitizer> |
fa19593551c6
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384 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
385 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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386 <param name="param_peak_options_pc_mz_range" type="text" size="30" value=":" label="MSn (n>=2) precursor filtering according to their m/z value" help="(-pc_mz_range) Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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387 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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388 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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389 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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390 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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391 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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392 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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393 </param> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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3
diff
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394 <repeat name="rep_param_peak_options_pc_mz_list" min="0" title="param_peak_options_pc_mz_list"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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395 <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept"> |
fa19593551c6
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|
396 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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397 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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398 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
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399 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
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|
400 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
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|
401 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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402 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
403 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff
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|
404 <repeat name="rep_param_peak_options_level" min="0" max="1" title="param_peak_options_level"> |
fa19593551c6
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diff
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|
405 <param name="param_peak_options_level" type="text" size="30" value="1 2 3" label="MS levels to extract" help="(-level) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
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|
406 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
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407 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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408 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
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409 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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410 </valid> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
411 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
412 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
413 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
414 <param name="param_peak_options_sort_peaks" display="radio" type="boolean" truevalue="-peak_options:sort_peaks" falsevalue="" checked="false" optional="True" label="Sorts the peaks according to m/z" help="(-sort_peaks) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
415 <param name="param_peak_options_no_chromatograms" display="radio" type="boolean" truevalue="-peak_options:no_chromatograms" falsevalue="" checked="false" optional="True" label="No conversion to space-saving real chromatograms," help="(-no_chromatograms) e.g. from SRM scans"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
416 <param name="param_peak_options_remove_chromatograms" display="radio" type="boolean" truevalue="-peak_options:remove_chromatograms" falsevalue="" checked="false" optional="True" label="Removes chromatograms stored in a file" help="(-remove_chromatograms) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
417 <param name="param_peak_options_mz_precision" display="radio" type="select" optional="False" value="64" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="(-mz_precision) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
418 <option value="32">32</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
419 <option value="64" selected="true">64</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
420 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
421 <param name="param_peak_options_int_precision" display="radio" type="select" optional="False" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
422 <option value="32" selected="true">32</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
423 <option value="64">64</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
424 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
425 <param name="param_peak_options_indexed_file" display="radio" type="boolean" truevalue="-peak_options:indexed_file" falsevalue="" checked="false" optional="True" label="Whether to add an index to the file when writing" help="(-indexed_file) "/> |
3
59adb20eb08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents:
1
diff
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426 <param name="param_peak_options_zlib_compression" display="radio" type="boolean" truevalue="-peak_options:zlib_compression" falsevalue="" checked="false" optional="True" label="Whether to store data with zlib compression (lossless compression)" help="(-zlib_compression) "/> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
427 <param name="param_peak_options_numpress_masstime" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
428 <option value="none" selected="true">none</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
429 <option value="linear">linear</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
430 <option value="pic">pic</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
431 <option value="slof">slof</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
432 </param> |
3
59adb20eb08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents:
1
diff
changeset
|
433 <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (default 10 ppm at 100 m/z; set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-masstime_error) "/> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
434 <param name="param_peak_options_numpress_intensity" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
435 <option value="none" selected="true">none</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
436 <option value="linear">linear</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
437 <option value="pic">pic</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
438 <option value="slof">slof</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
439 </param> |
3
59adb20eb08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents:
1
diff
changeset
|
440 <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-intensity_error) "/> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
441 <param name="param_spectra_remove_zoom" display="radio" type="boolean" truevalue="-spectra:remove_zoom" falsevalue="" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
442 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
443 <option value="Unknown">Unknown</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
444 <option value="MassSpectrum">MassSpectrum</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
445 <option value="MS1Spectrum">MS1Spectrum</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
446 <option value="MSnSpectrum">MSnSpectrum</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
447 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
448 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
449 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
450 <option value="ConstantNeutralGain">ConstantNeutralGain</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
451 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
452 <option value="Precursor">Precursor</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
453 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
454 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
455 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
456 <option value="Emission">Emission</option> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
3
diff
changeset
|
457 <option value="Absorption">Absorption</option> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
458 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
459 <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
460 <option value="Collision-induced dissociation">Collision-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
461 <option value="Post-source decay">Post-source decay</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
462 <option value="Plasma desorption">Plasma desorption</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
463 <option value="Surface-induced dissociation">Surface-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
464 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
465 <option value="Electron capture dissociation">Electron capture dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
466 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
467 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
468 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
469 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
470 <option value="Photodissociation">Photodissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
471 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
472 <option value="Pulsed q dissociation">Pulsed q dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
473 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
474 <param name="param_spectra_remove_collision_energy" type="text" size="30" value=":" label="Remove MSn scans with a collision energy in the given interval" help="(-remove_collision_energy) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
475 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
476 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
477 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
478 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
479 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
480 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
481 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
482 <param name="param_spectra_remove_isolation_window_width" type="text" size="30" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="(-remove_isolation_window_width) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
483 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
484 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
485 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
486 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
487 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
488 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
489 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
490 <param name="param_spectra_select_zoom" display="radio" type="boolean" truevalue="-spectra:select_zoom" falsevalue="" checked="false" optional="True" label="Select zoom (enhanced resolution) scans" help="(-select_zoom) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
491 <param name="param_spectra_select_mode" type="select" optional="True" label="Selects scans by scan mode" help="(-select_mode) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
492 <option value="Unknown">Unknown</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
493 <option value="MassSpectrum">MassSpectrum</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
494 <option value="MS1Spectrum">MS1Spectrum</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
495 <option value="MSnSpectrum">MSnSpectrum</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
496 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
497 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
498 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
499 <option value="ConstantNeutralGain">ConstantNeutralGain</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
500 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
501 <option value="Precursor">Precursor</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
502 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
503 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
504 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
505 <option value="Emission">Emission</option> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
3
diff
changeset
|
506 <option value="Absorption">Absorption</option> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
507 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
508 <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
509 <option value="Collision-induced dissociation">Collision-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
510 <option value="Post-source decay">Post-source decay</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
511 <option value="Plasma desorption">Plasma desorption</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
512 <option value="Surface-induced dissociation">Surface-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
513 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
514 <option value="Electron capture dissociation">Electron capture dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
515 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
516 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
517 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
518 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
519 <option value="Photodissociation">Photodissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
520 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
521 <option value="Pulsed q dissociation">Pulsed q dissociation</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
522 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
523 <param name="param_spectra_select_collision_energy" type="text" size="30" value=":" label="Select MSn scans with a collision energy in the given interval" help="(-select_collision_energy) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
524 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
525 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
526 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
527 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
528 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
529 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
530 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
531 <param name="param_spectra_select_isolation_window_width" type="text" size="30" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="(-select_isolation_window_width) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
532 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
533 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
534 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
535 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
536 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
537 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
538 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
539 <param name="param_spectra_select_polarity" display="radio" type="select" optional="True" label="Retain MSn scans with a certain scan polarity" help="(-select_polarity) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
540 <option value="unknown">unknown</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
541 <option value="positive">positive</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
542 <option value="negative">negative</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
543 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
544 <param name="param_feature_q" type="text" size="30" value=":" label="Overall quality range to extract [0:1]" help="(-q) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
545 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
546 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
547 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
548 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
549 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
550 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
551 </param> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
3
diff
changeset
|
552 <repeat name="rep_param_consensus_map" min="0" title="param_consensus_map"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
553 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
554 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
555 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
556 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
557 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
558 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
559 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
560 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
561 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
562 <param name="param_consensus_map_and" display="radio" type="boolean" truevalue="-consensus:map_and" falsevalue="" checked="false" optional="True" label="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" help="(-map_and) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
563 <param name="param_consensus_blackorwhitelist_blacklist" display="radio" type="select" optional="False" value="true" label="True: remove matched MS2" help="(-blacklist) False: retain matched MS2 spectra. Other levels are kept"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
564 <option value="false">false</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
changeset
|
565 <option value="true" selected="true">true</option> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
566 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
567 <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! <br>Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) <br>If consensus:blackorwhitelist:maps is specified, only these will be used. <br>"/> |
7
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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parents:
3
diff
changeset
|
568 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" title="param_consensus_blackorwhitelist_maps"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
569 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
570 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
571 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
572 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
573 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
574 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
575 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
576 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
577 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
578 <param name="param_consensus_blackorwhitelist_rt" type="float" min="0.0" optional="True" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help="(-rt) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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|
579 <param name="param_consensus_blackorwhitelist_mz" type="float" min="0.0" optional="True" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help="(-mz) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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580 <param name="param_consensus_blackorwhitelist_use_ppm_tolerance" display="radio" type="boolean" truevalue="-consensus:blackorwhitelist:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If ppm tolerance should be used" help="(-use_ppm_tolerance) Otherwise Da are used"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
581 <param name="param_f_and_c_charge" type="text" size="30" value=":" label="Charge range to extract" help="(-charge) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
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changeset
|
582 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff
changeset
|
583 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
584 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
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|
585 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
586 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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changeset
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587 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
588 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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changeset
|
589 <param name="param_f_and_c_size" type="text" size="30" value=":" label="Size range to extract" help="(-size) "> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
590 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
591 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
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|
592 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
593 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
594 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
595 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
596 </param> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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3
diff
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|
597 <repeat name="rep_param_f_and_c_remove_meta" min="0" title="param_f_and_c_remove_meta"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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|
598 <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
599 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
600 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
601 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
602 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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changeset
|
603 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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changeset
|
604 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
605 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
606 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
607 <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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3
diff
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|
608 <repeat name="rep_param_id_sequences_whitelist" min="0" title="param_id_sequences_whitelist"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
609 <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
610 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
611 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
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|
612 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
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|
613 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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614 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
changeset
|
615 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff
changeset
|
616 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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|
617 </repeat> |
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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3
diff
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|
618 <repeat name="rep_param_id_accessions_whitelist" min="0" title="param_id_accessions_whitelist"> |
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
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|
619 <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
620 <sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
621 <valid initial="string.printable"> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
622 <remove value="'"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
623 <remove value="""/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
changeset
|
624 </valid> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
625 </sanitizer> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
626 </param> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
627 </repeat> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
628 <param name="param_id_remove_annotated_features" display="radio" type="boolean" truevalue="-id:remove_annotated_features" falsevalue="" checked="false" optional="True" label="Remove features with annotations" help="(-remove_annotated_features) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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|
629 <param name="param_id_remove_unannotated_features" display="radio" type="boolean" truevalue="-id:remove_unannotated_features" falsevalue="" checked="false" optional="True" label="Remove features without annotations" help="(-remove_unannotated_features) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
630 <param name="param_id_remove_unassigned_ids" display="radio" type="boolean" truevalue="-id:remove_unassigned_ids" falsevalue="" checked="false" optional="True" label="Remove unassigned peptide identifications" help="(-remove_unassigned_ids) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
631 <param name="param_id_blacklist" type="data" format="idxml" optional="True" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file! <br>Matching tolerances are taken from 'id:rt' and 'id:mz' options" help="(-blacklist) <br>This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches"/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
632 <param name="param_id_rt" type="float" min="0.0" optional="True" value="0.1" label="Retention tolerance [s] for precursor to id position" help="(-rt) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
633 <param name="param_id_mz" type="float" min="0.0" optional="True" value="0.001" label="m/z tolerance [Th] for precursor to id position" help="(-mz) "/> |
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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634 <param name="param_id_blacklist_imperfect" display="radio" type="boolean" truevalue="-id:blacklist_imperfect" falsevalue="" checked="false" optional="True" label="Allow for mismatching precursor positions (see 'id:blacklist')" help="(-blacklist_imperfect) "/> |
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635 <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> |
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636 <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> |
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637 <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/> |
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638 <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) "> |
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639 <option value="true" selected="true">true</option> |
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640 <option value="false">false</option> |
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641 </param> |
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642 <expand macro="advanced_options"> |
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643 <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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644 <param name="param_id_remove_clashes" display="radio" type="boolean" truevalue="-id:remove_clashes" falsevalue="" checked="false" optional="True" label="Remove features with id clashes (different sequences mapped to one feature)" help="(-remove_clashes) "/> |
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645 <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> |
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646 <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/> |
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647 <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/> |
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648 <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/> |
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649 <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> |
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650 </expand> |
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651 </inputs> |
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652 <outputs> |
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653 <data name="param_out" metadata_source="param_in" format="input"/> |
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654 </outputs> |
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655 <help>Extracts or manipulates portions of data from peak, feature or consensus-feature files. |
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656 |
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657 |
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658 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html</help> |
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659 </tool> |