Mercurial > repos > jjohnson > encyclopedia_fasta_to_prosit_csv

annotate macros.xml @ 3:b9a2af09b828 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"
author jjohnson
date Thu, 02 Jul 2020 11:14:11 -0400
parents 725e83e1eed1
children 91343296dbff
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d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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1 <macros>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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2 <token name="@VERSION@">0.9.5</token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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3 <xml name="requirements">
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4 <requirements>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
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6 <yield/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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7 </requirements>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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8 </xml>
2
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9
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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10 <token name="@ENCYCLOPEDIA_WIKI@">
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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11 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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12
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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14 </token>
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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15 <xml name="citations">
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16 <citations>
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17 <citation type="doi">10.1038/s41467-018-07454-w</citation>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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18 <citation type="doi">10.1038/s41467-020-15346-1</citation>
1
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19 <citation type="doi">10.1074/mcp.P119.001913</citation>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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20 <yield/>
0
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21 </citations>
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22 </xml>
2
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23
0
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24 <token name="@CMD_IMPORTS@">
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25 #import re
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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26 #def identifier_or_name($input1)
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27 #if hasattr($input1, 'element_identifier')
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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28 #return $input1.element_identifier
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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29 #else
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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30 #return $input1.name
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31 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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32 #end def
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33 #def clean($name1)
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34 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz'))))
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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35 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz')))
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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36 #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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37 #return $name_clean
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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38 #end def
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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39 #def ln_name($ds)
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40 #set $ext = ''
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41 #if $ds.is_of_type('mzml')
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42 #set $ext = ".mzML"
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43 #else if $ds.is_of_type('elib')
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44 #set $ext = ".elib"
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45 #else if $ds.is_of_type('dlib')
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46 #set $ext = ".dlib"
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47 #else if $ds.is_of_type('blib')
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48 #set $ext = ".blib"
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49 #else if $ds.is_of_type('fasta')
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50 #set $ext = ".fasta"
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51 #else if $ds.is_of_type('fasta.gz')
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52 #set $ext = ".fasta.gz"
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53 #end if
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54 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
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55 #return $name
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56 #end def
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57 #set $i_name = None
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58 #set $f_name = None
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59 #set $l_name = None
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60 #set $t_name = None
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61 </token>
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62
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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63 <xml name="scan_input">
1
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64 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
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65 <help>@MSCONVERT_RAW@</help>
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66 </param>
0
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67 </xml>
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68 <token name="@LINK_SCAN_INPUT@"><![CDATA[
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69 #set $i_name = $ln_name($i)
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70 ln -s '$i' '$i_name' &&
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71 ]]></token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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72 <token name="@SCAN_INPUT@">
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73 -i '$i_name'
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74 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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75
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76 <xml name="scan_inputs">
1
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77 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
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78 <help>@MSCONVERT_RAW@</help>
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79 </param>
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
80 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
81 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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82 #set $inputs_dir = 'inputs'
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
83 mkdir -p $inputs_dir &&
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
84 #for $sf in $i
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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85 #set $i_name = $ln_name($sf)
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
86 ln -s '$sf' '${inputs_dir}/${i_name}' &&
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
87 #end for
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
88 ]]></token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
89 <token name="@SCAN_INPUTS@">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
90 -i '$inputs_dir'
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
91 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
92
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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93 <xml name="fasta_input">
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
parents: 0
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94 <param argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
parents: 0
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95 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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96 </param>
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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97 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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98 <token name="@LINK_FASTA_INPUT@"><![CDATA[
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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99 #set $f_name = $ln_name($f)
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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100 ln -s '$f' '$f_name' &&
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
101 ]]></token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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102 <token name="@FASTA_INPUT@">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
103 -f '$f_name'
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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104 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
105
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
106 <xml name="target_fasta">
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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107 <param argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/>
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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108 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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109 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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110 <token name="@LINK_TARGET_FASTA@"><![CDATA[
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
111 #if $t
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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112 #set $t_name = $ln_name($t)
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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113 ln -s '$t' '$t_name' &&
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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114 #else
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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115 #set $t_name = None
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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116 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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117 ]]></token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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118 <token name="@TARGET_FASTA@">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
119 #if $t_name
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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120 -t '$t_name'
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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121 -tp $tp
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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122 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
123 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
124
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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diff changeset
125 <xml name="lib_input" token_optional="true" token_libhelp="">
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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126 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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127 <help>@LIBHELP@</help>
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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128 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
129 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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130 <token name="@LINK_LIB_INPUT@"><![CDATA[
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
131 #if $l
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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132 #set $l_name = $ln_name($l)
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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133 cp '$l' $l_name &&
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
134 #else
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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135 #set $l_name = None
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
136 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
137 ]]></token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
138 <token name="@LIB_INPUT@">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
139 #if $l_name
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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140 -l '$l_name'
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
141 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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142 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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143
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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144 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false"
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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145 token_cid_selected="false" token_hcd_selected="false">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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146 <conditional name="acquisition">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
147 <param name="set_acquisition" type="select" label="Set Acquisition Options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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148 <option value="no">No - use default options</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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149 <option value="yes">Yes</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
150 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
151 <when value="no"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
152 <when value="yes">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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153 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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154 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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155 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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156 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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157 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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158 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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159 <option value="Trypsin">Trypsin</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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160 <option value="Trypsin/p">Trypsin/p</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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161 <option value="Lys-C">Lys-C</option>
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162 <option value="Lys-N">Lys-N</option>
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163 <option value="Arg-C">Arg-C</option>
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164 <option value="Glu-C">Glu-C</option>
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165 <option value="Chymotrypsin">Chymotrypsin</option>
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166 <option value="Pepsin A">Pepsin A</option>
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167 <option value="Elastase">Elastase</option>
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168 <option value="Thermolysin">Thermolysin</option>
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169 <option value="No Enzyme">No Enzyme</option>
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170 </param>
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171 <param argument="-frag" type="select" optional="true" label="Fragmentation">
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172 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option>
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173 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option>
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174 <option value="ETD">ETD (C/Z/Z+1)</option>
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175 </param>
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176 </when>
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177 </conditional>
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178 </xml>
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179 <xml name="encyclopedia_common_options">
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180 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false"
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181 token_cid_selected="true" token_hcd_selected="false"/>
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182 </xml>
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183 <xml name="walnut_common_options">
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184 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
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185 token_cid_selected="false" token_hcd_selected="true"/>
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186 </xml>
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187 <token name="@COMMON_OPTIONS@">
2
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188 #if $options.acquisition.set_acquisition == 'yes'
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189 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
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190 #if $options.acquisition.acquisition
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191 -acquisition '$options.acquisition.acquisition'
0
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192 #end if
2
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193 #if $options.acquisition.enzyme:
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194 -enzyme '$options.acquisition.enzyme'
0
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195 #end if
2
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196 #if $options.acquisition.frag:
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197 -frag '$options.acquisition.frag'
0
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198 #end if
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199 #end if
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200 </token>
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201
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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202 <xml name="mass_tolerance">
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203 <conditional name="tolerance">
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204 <param name="set_tolerance" type="select" label="Set Tolerance Options">
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205 <option value="no">No - use default options</option>
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206 <option value="yes">Yes</option>
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207 </param>
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208 <when value="no"/>
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209 <when value="yes">
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210 <conditional name="precursor_tolerance">
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211 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
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212 <option value="PPM">PPM</option>
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213 <option value="AMU">AMU</option>
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214 <option value="Resolution">Resolution</option>
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215 </param>
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216 <when value="PPM">
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217 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
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218 </when>
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219 <when value="AMU">
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220 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
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221 </when>
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222 <when value="Resolution">
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223 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
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224 </when>
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225 </conditional>
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226 <conditional name="fragment_tolerance">
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227 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
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228 <option value="PPM">PPM</option>
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229 <option value="AMU">AMU</option>
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230 <option value="Resolution">Resolution</option>
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231 </param>
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232 <when value="PPM">
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233 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
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234 </when>
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235 <when value="AMU">
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236 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
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237 </when>
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238 <when value="Resolution">
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239 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
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240 </when>
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241 </conditional>
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242 <yield/>
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243 </when>
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244 </conditional>
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245 </xml>
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246 <token name="@MASS_TOLERANCE@">
2
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247 #if $options.tolerance.set_tolerance == 'yes'
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248 -ptolunits $options.tolerance.precursor_tolerance.ptolunits
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249 -ptol $options.tolerance.precursor_tolerance.ptol
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250 -ftolunits $options.tolerance.fragment_tolerance.ftolunits
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251 -ftol $options.tolerance.fragment_tolerance.ftol
0
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252 #end if
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253 </token>
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254
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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255 <xml name="mass_library_tolerance">
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256 <expand macro="mass_tolerance">
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257 <conditional name="library_tolerance">
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258 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
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259 <option value="defaults">Use defaults</option>
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260 <option value="PPM">PPM</option>
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261 <option value="AMU">AMU</option>
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262 <option value="Resolution">Resolution</option>
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263 </param>
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264 <when value="defaults"/>
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265 <when value="PPM">
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266 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
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267 </when>
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268 <when value="AMU">
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269 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
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270 </when>
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271 <when value="Resolution">
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272 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
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273 </when>
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274 </conditional>
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275 </expand>
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276 </xml>
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277 <token name="@MASS_LIBRARY_TOLERANCE@">
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278 @MASS_TOLERANCE@
2
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279 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
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280 -ltolunits $options.tolerance.library_tolerance.ltolunits
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281 -ltol $options.tolerance.library_tolerance.ltol
0
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282 #end if
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283 </token>
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284
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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285 <xml name="percolator_options">
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286 <conditional name="percolator">
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287 <param name="set_percolator" type="select" label="Set Percolator Options">
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288 <option value="no">No - use default options</option>
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289 <option value="yes">Yes</option>
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290 </param>
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291 <when value="no"/>
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292 <when value="yes">
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293 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
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294 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
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295 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
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296 </when>
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297 </conditional>
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298 </xml>
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299 <token name="@PERCOLATOR_OPTIONS@">
2
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300 #if $options.percolator.set_percolator == 'yes'
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301 #if str($options.percolator.percolatorVersionNumber)
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302 -percolatorVersionNumber $options.percolator.percolatorVersionNumber
0
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303 #end if
2
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304 #if str($options.percolator.percolatorProteinThreshold)
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305 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
0
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306 #end if
2
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307 #if str($options.percolator.percolatorThreshold)
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308 -percolatorThreshold $options.percolator.percolatorThreshold
0
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309 #end if
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310 #end if
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311 </token>
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312
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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313 <xml name="peak_options">
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314 <conditional name="peak">
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315 <param name="set_peak" type="select" label="Set Peak Options">
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316 <option value="no">No - use default options</option>
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317 <option value="yes">Yes</option>
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318 </param>
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319 <when value="no"/>
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320 <when value="yes">
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321 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/>
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322 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/>
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323 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
324 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
325 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
326 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
327 <option value="false">No</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
328 <option value="true">Yes</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
329 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
330 </when>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
331 </conditional>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
332 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
333 <token name="@PEAK_OPTIONS@">
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
334 #if $options.peak.set_peak == 'yes'
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
335 #if str($options.peak.numberOfQuantitativePeaks)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
336 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
337 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
338 #if str($options.peak.minNumOfQuantitativePeaks)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
339 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
340 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
341 #if str($options.peak.minQuantitativeIonNumber)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
342 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
343 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
344 #if str($options.peak.minIntensity)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
345 -minIntensity $options.peak.minIntensity
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
346 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
347 #if str($options.peak.expectedPeakWidth)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
348 -expectedPeakWidth $options.peak.expectedPeakWidth
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
349 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
350 #if $options.peak.filterPeaklists
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
351 -filterPeaklists $options.peak.filterPeaklists
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
352 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
353 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
354 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
355
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
356 <xml name="window_options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
357 <conditional name="window">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
358 <param name="set_window" type="select" label="Set Window Options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
359 <option value="no">No - use default options</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
360 <option value="yes">Yes</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
361 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
362 <when value="no"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
363 <when value="yes">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
364 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
365 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
366 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
367 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
368 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
369 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
370 <option value="window">Across entire window</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
371 <option value="recal20">Recalibrated (20% gradient)</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
372 <option value="recal">Recalibrated (peak width only)</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
373 <option value="uncal20">Uncalibrated (20% gradient)</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
374 <option value="uncal">Uncalibrated (peak width only)</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
375 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
376 </when>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
377 </conditional>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
378 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
379 <token name="@WINDOW_OPTIONS@">
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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380 #if $options.window.set_window == 'yes'
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
381 #if str($options.window.foffset)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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382 -foffset $options.window.foffset
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
383 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
384 #if str($options.window.poffset)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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385 -poffset $options.window.poffset
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
386 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
387 #if str($options.window.precursorIsolationMargin)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
388 -precursorIsolationMargin $options.window.precursorIsolationMargin
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
389 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
390 #if str($options.window.precursorWindowSize)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
391 -precursorWindowSize $options.window.precursorWindowSize
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
392 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
393 #if str($options.window.rtWindowInMin)
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
394 -rtWindowInMin $options.window.rtWindowInMin
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
395 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
396 #if $options.window.scoringBreadthType
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
397 -scoringBreadthType $options.window.scoringBreadthType
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
398 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
399 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
400 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
401
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
402 <xml name="modification_options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
403 <conditional name="modifications">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
404 <param name="set_modifications" type="select" label="Set Modifications Options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
405 <option value="no">No - use default options</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
406 <option value="yes">Yes</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
407 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
408 <when value="no"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
409 <when value="yes">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
410 <param argument="-fixed" type="select" optional="true" label="Fixed Modification">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
411 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
412 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
413 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
414 <option value="C=125.047679">C+125 (NEM) C=125.047679</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
415 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
416 <yield/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
417 <!--
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
418 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
419 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
420 -->
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
421 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
422 </when>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
423 </conditional>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
424 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
425 <token name="@MODIFICATION_OPTIONS@">
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
426 #if $options.modifications.set_modifications == 'yes'
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
427 #if $options.modifications.fixed
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
428 -fixed $options.modifications.fixed
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
429 #end if
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
430 -verifyModificationIons $options.modifications.verifyModificationIons
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
431 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
432 </token>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
433
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
434 <xml name="search_options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
435 <conditional name="search">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
436 <param name="set_search" type="select" label="Set Search Options">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
437 <option value="no">No - use default options</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
438 <option value="yes">Yes</option>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
439 </param>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
440 <when value="no"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
441 <when value="yes">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
442 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
443 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
444 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
445 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
446 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
447 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
448 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
449 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
450 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
451 <!--
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
452 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
453 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
454 -->
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
455 </when>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
456 </conditional>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
457 </xml>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
458 <token name="@SEARCH_OPTIONS@">
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
459 #if $options.search.set_search == 'yes'
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
460 -minCharge $options.search.minCharge
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
461 -maxCharge $options.search.maxCharge
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
462 -minLength $options.search.minLength
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
463 -maxLength $options.search.maxLength
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
464 -minEluteTime $options.search.minEluteTime
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
465 -maxMissedCleavage $options.search.maxMissedCleavage
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
466 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
467 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
468 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
469 ## -addDecoysToBackground $options.search.addDecoysToBackground
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
470 ## -dontRunDecoys $options.search.dontRunDecoys
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
471 #end if
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
472 </token>
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
473
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
474 <xml name="options_section">
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
475 <section name="options" title="Parameter Settings" expanded="false">
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
476 <expand macro="common_options"/>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
477 <expand macro="mass_library_tolerance"/>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
478 <expand macro="percolator_options"/>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
479 <expand macro="peak_options"/>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
480 <expand macro="window_options"/>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
481 <expand macro="modification_options"/>
3
b9a2af09b828 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"
jjohnson
parents: 2
diff changeset
482 <expand macro="search_options"/>
2
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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483 </section>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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484 </xml>
725e83e1eed1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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485
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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486 <xml name="libexport">
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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487 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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488 </xml>
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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489 <token name="@MSCONVERT_CMD@"><![CDATA[
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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490 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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491 ]]>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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492 </token>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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493 <token name="@MSCONVERT_RAW@"><![CDATA[
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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494 mzML conversion from RAW requires special options: @MSCONVERT_CMD@
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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495 ]]>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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496 </token>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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497 <token name="@MSCONVERT_HELP@"><![CDATA[
0
d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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498
1
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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499 The MSConvert command can be used to deconvolute DIA raw files. You need to use these options
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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500
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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501 ::
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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502
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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503 @MSCONVERT_CMD@
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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504
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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505 ]]>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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506 </token>
c394bccd6f64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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507 </macros>