Mercurial > repos > galaxyp > encyclopedia_quantify

annotate macros.xml @ 1:1c5cbf8f79ce 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 64740168b7816f0fe38f6f0629cb7e618cd42878"
author galaxyp
date Thu, 08 Apr 2021 17:55:50 +0000
parents 4081e4faa4ab
children 0fa397f4f40b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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1 <macros>
1
1c5cbf8f79ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 64740168b7816f0fe38f6f0629cb7e618cd42878"
galaxyp
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2 <token name="@TOOL_VERSION@">1.2.2</token>
1c5cbf8f79ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 64740168b7816f0fe38f6f0629cb7e618cd42878"
galaxyp
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3 <token name="@VERSION_SUFFIX@">0</token>
0
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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4 <xml name="requirements">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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5 <requirements>
1
1c5cbf8f79ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 64740168b7816f0fe38f6f0629cb7e618cd42878"
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6 <requirement type="package" version="@TOOL_VERSION@">encyclopedia</requirement>
0
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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7 <yield/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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8 </requirements>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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9 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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10
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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11 <token name="@ENCYCLOPEDIA_WIKI@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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12 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. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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13
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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14 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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15 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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16 <xml name="citations">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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17 <citations>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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18 <citation type="doi">10.1038/s41467-018-07454-w</citation>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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19 <citation type="doi">10.1038/s41467-020-15346-1</citation>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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20 <citation type="doi">10.1074/mcp.P119.001913</citation>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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21 <yield/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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22 </citations>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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23 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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24
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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25 <token name="@CMD_IMPORTS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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26 #import re
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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27 #def identifier_or_name($input1)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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28 #if hasattr($input1, 'element_identifier')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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29 #return $input1.element_identifier
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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30 #else
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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31 #return $input1.name
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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32 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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33 #end def
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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34 #def clean($name1)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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35 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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36 #return $name_clean
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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37 #end def
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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38 #def ln_name($ds)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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39 #set $ext = ''
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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40 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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41 #set $ext = ".mzML"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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42 #else if $ds.is_of_type('elib')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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43 #set $ext = ".elib"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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44 #else if $ds.is_of_type('dlib')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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45 #set $ext = ".dlib"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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46 #else if $ds.is_of_type('blib')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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47 #set $ext = ".blib"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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48 #else if $ds.is_of_type('fasta')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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49 #set $ext = ".fasta"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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50 #else if $ds.is_of_type('fasta.gz')
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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51 #set $ext = ".fasta.gz"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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52 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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53 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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54 #return $name
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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55 #end def
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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56 #set $i_name = None
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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57 #set $f_name = None
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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58 #set $l_name = None
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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59 #set $t_name = None
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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60 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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61
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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62 <xml name="scan_input">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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63 <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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64 <help>@MSCONVERT_RAW@</help>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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65 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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66 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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67 <token name="@LINK_SCAN_INPUT@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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68 #set $i_name = $ln_name($scan_input)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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69 ln -s '$scan_input' '$i_name' &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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70 ]]></token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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71 <token name="@SCAN_INPUT@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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72 -i '$i_name'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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73 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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74
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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75 <xml name="scan_inputs">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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76 <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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77 <help>@MSCONVERT_RAW@</help>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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78 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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79 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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80 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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81 #set $inputs_dir = 'inputs'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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diff changeset
82 mkdir -p $inputs_dir &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
83 #for $sf in $scan_inputs
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
84 #set $i_name = $ln_name($sf)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
85 ln -s '$sf' '${inputs_dir}/${i_name}' &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
86 #end for
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
87 ]]></token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
88 <token name="@SCAN_INPUTS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
89 -i '$inputs_dir'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
90 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
91
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
92 <xml name="fasta_input">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
93 <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
94 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
95 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
96 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
97 <token name="@LINK_FASTA_INPUT@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
98 #set $f_name = $ln_name($fasta)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
99 ln -s '$fasta' '$f_name' &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
100 ]]></token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
101 <token name="@FASTA_INPUT@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
102 -f '$f_name'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
103 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
104
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
105 <xml name="target_fasta">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
106 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
107 <help>Optional - Only analyze this subset of the background fasta proteome</help>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
108 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
109 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
110 <help>Rather than full proteins</help>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
111 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
112 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
113 <token name="@LINK_TARGET_FASTA@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
114 #if $target_fasta
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
115 #set $t_name = $ln_name($target_fasta)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
116 ln -s '$target_fasta' '$t_name' &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
117 #else
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
118 #set $t_name = None
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
119 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
120 ]]></token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
121 <token name="@TARGET_FASTA@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
122 #if $t_name
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
123 -t '$t_name'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
124 -tp $tp
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
125 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
126 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
127
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
128 <xml name="lib_input" token_optional="true" token_libhelp="">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
129 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
130 <help>@LIBHELP@</help>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
131 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
132 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
133 <token name="@LINK_LIB_INPUT@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
134 #if $library
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
135 #set $l_name = $ln_name($library)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
136 cp '$library' '$l_name' &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
137 #else
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
138 #set $l_name = None
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
139 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
140 ]]></token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
141 <token name="@LIB_INPUT@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
142 #if $l_name
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
143 -l '$l_name'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
144 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
145 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
146
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
147 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
148 token_cid_selected="false" token_hcd_selected="false">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
149 <conditional name="acquisition">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
150 <param name="set_acquisition" type="select" label="Set Acquisition Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
151 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
152 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
153 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
154 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
155 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
156 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
157 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
158 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
159 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
160 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
161 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
162 <option value="Trypsin">Trypsin</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
163 <option value="Trypsin/p">Trypsin/p</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
164 <option value="Lys-C">Lys-C</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
165 <option value="Lys-N">Lys-N</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
166 <option value="Arg-C">Arg-C</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
167 <option value="Glu-C">Glu-C</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
168 <option value="Chymotrypsin">Chymotrypsin</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
169 <option value="Pepsin A">Pepsin A</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
170 <option value="Elastase">Elastase</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
171 <option value="Thermolysin">Thermolysin</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
172 <option value="No Enzyme">No Enzyme</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
173 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
174 <param argument="-frag" type="select" optional="true" label="Fragmentation">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
175 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
176 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
177 <option value="ETD">ETD (C/Z/Z+1)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
178 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
179 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
180 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
181 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
182 <xml name="encyclopedia_common_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
183 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
184 token_cid_selected="true" token_hcd_selected="false"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
185 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
186 <xml name="walnut_common_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
187 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
188 token_cid_selected="false" token_hcd_selected="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
189 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
190 <token name="@COMMON_OPTIONS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
191 #if $options.acquisition.set_acquisition == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
192 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
193 #if $options.acquisition.acquisition
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
194 -acquisition '$options.acquisition.acquisition'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
195 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
196 #if $options.acquisition.enzyme:
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
197 -enzyme '$options.acquisition.enzyme'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
198 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
199 #if $options.acquisition.frag:
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
200 -frag '$options.acquisition.frag'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
201 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
202 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
203 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
204
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
205 <xml name="mass_tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
206 <conditional name="tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
207 <param name="set_tolerance" type="select" label="Set Tolerance Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
208 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
209 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
210 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
211 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
212 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
213 <conditional name="precursor_tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
214 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
215 <option value="PPM">PPM</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
216 <option value="AMU">AMU</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
217 <option value="Resolution">Resolution</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
218 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
219 <when value="PPM">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
220 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
221 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
222 <when value="AMU">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
223 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
224 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
225 <when value="Resolution">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
226 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
227 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
228 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
229 <conditional name="fragment_tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
230 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
231 <option value="PPM">PPM</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
232 <option value="AMU">AMU</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
233 <option value="Resolution">Resolution</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
234 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
235 <when value="PPM">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
236 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
237 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
238 <when value="AMU">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
239 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
240 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
241 <when value="Resolution">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
242 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
243 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
244 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
245 <yield/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
246 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
247 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
248 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
249 <token name="@MASS_TOLERANCE@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
250 #if $options.tolerance.set_tolerance == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
251 -ptolunits $options.tolerance.precursor_tolerance.ptolunits
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
252 -ptol $options.tolerance.precursor_tolerance.ptol
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
253 -ftolunits $options.tolerance.fragment_tolerance.ftolunits
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
254 -ftol $options.tolerance.fragment_tolerance.ftol
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
255 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
256 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
257
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
258 <xml name="mass_library_tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
259 <expand macro="mass_tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
260 <conditional name="library_tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
261 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
262 <option value="defaults">Use defaults</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
263 <option value="PPM">PPM</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
264 <option value="AMU">AMU</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
265 <option value="Resolution">Resolution</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
266 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
267 <when value="defaults"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
268 <when value="PPM">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
269 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
270 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
271 <when value="AMU">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
272 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
273 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
274 <when value="Resolution">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
275 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
276 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
277 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
278 </expand>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
279 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
280 <token name="@MASS_LIBRARY_TOLERANCE@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
281 @MASS_TOLERANCE@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
282 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
283 -ltolunits $options.tolerance.library_tolerance.ltolunits
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
284 -ltol $options.tolerance.library_tolerance.ltol
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
285 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
286 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
287
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
288 <xml name="percolator_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
289 <conditional name="percolator">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
290 <param name="set_percolator" type="select" label="Set Percolator Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
291 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
292 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
293 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
294 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
295 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
296 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
297 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
298 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
299 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
300 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
301 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
302 <token name="@PERCOLATOR_OPTIONS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
303 #if $options.percolator.set_percolator == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
304 #if str($options.percolator.percolatorVersionNumber)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
305 -percolatorVersionNumber $options.percolator.percolatorVersionNumber
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
306 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
307 #if str($options.percolator.percolatorProteinThreshold)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
308 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
309 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
310 #if str($options.percolator.percolatorThreshold)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
311 -percolatorThreshold $options.percolator.percolatorThreshold
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
312 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
313 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
314 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
315
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
316 <xml name="peak_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
317 <conditional name="peak">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
318 <param name="set_peak" type="select" label="Set Peak Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
319 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
320 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
321 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
322 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
323 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
324 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
325 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
326 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
327 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
328 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
329 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
330 <option value="false">No</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
331 <option value="true">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
332 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
333 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
334 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
335 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
336 <token name="@PEAK_OPTIONS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
337 #if $options.peak.set_peak == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
338 #if str($options.peak.numberOfQuantitativePeaks)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
339 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
340 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
341 #if str($options.peak.minNumOfQuantitativePeaks)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
342 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
343 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
344 #if str($options.peak.minQuantitativeIonNumber)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
345 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
346 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
347 #if str($options.peak.minIntensity)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
348 -minIntensity $options.peak.minIntensity
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
349 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
350 #if str($options.peak.expectedPeakWidth)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
351 -expectedPeakWidth $options.peak.expectedPeakWidth
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
352 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
353 #if $options.peak.filterPeaklists
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
354 -filterPeaklists $options.peak.filterPeaklists
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
355 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
356 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
357 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
358
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
359 <xml name="window_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
360 <conditional name="window">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
361 <param name="set_window" type="select" label="Set Window Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
362 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
363 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
364 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
365 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
366 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
367 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
368 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
369 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
370 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
371 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
372 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
373 <option value="window">Across entire window</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
374 <option value="recal20">Recalibrated (20% gradient)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
375 <option value="recal">Recalibrated (peak width only)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
376 <option value="uncal20">Uncalibrated (20% gradient)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
377 <option value="uncal">Uncalibrated (peak width only)</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
378 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
379 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
380 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
381 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
382 <token name="@WINDOW_OPTIONS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
383 #if $options.window.set_window == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
384 #if str($options.window.foffset)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
385 -foffset $options.window.foffset
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
386 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
387 #if str($options.window.poffset)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
388 -poffset $options.window.poffset
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
389 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
390 #if str($options.window.precursorIsolationMargin)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
391 -precursorIsolationMargin $options.window.precursorIsolationMargin
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
392 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
393 #if str($options.window.precursorWindowSize)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
394 -precursorWindowSize $options.window.precursorWindowSize
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
395 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
396 #if str($options.window.rtWindowInMin)
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
397 -rtWindowInMin $options.window.rtWindowInMin
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
398 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
399 #if $options.window.scoringBreadthType
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
400 -scoringBreadthType $options.window.scoringBreadthType
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
401 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
402 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
403 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
404
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
405 <xml name="modification_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
406 <conditional name="modifications">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
407 <param name="set_modifications" type="select" label="Set Modifications Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
408 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
409 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
410 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
411 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
412 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
413 <param argument="-fixed" type="select" optional="true" label="Fixed Modification">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
414 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
415 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
416 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
417 <option value="C=125.047679">C+125 (NEM) C=125.047679</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
418 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
419 <yield/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
420 <!--
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
421 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
422 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
423 -->
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
424 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
425 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
426 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
427 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
428 <token name="@MODIFICATION_OPTIONS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
429 #if $options.modifications.set_modifications == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
430 #if $options.modifications.fixed
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
431 -fixed $options.modifications.fixed
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
432 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
433 -verifyModificationIons $options.modifications.verifyModificationIons
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
434 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
435 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
436
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
437 <xml name="search_options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
438 <conditional name="search">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
439 <param name="set_search" type="select" label="Set Search Options">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
440 <option value="no">No - use default options</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
441 <option value="yes">Yes</option>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
442 </param>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
443 <when value="no"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
444 <when value="yes">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
445 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
446 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
447 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
448 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
449 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
450 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
451 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
452 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
453 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
454 <!--
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
455 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
456 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
457 -->
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
458 </when>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
459 </conditional>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
460 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
461 <token name="@SEARCH_OPTIONS@">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
462 #if $options.search.set_search == 'yes'
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
463 -minCharge $options.search.minCharge
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
464 -maxCharge $options.search.maxCharge
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
465 -minLength $options.search.minLength
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
466 -maxLength $options.search.maxLength
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
467 -minEluteTime $options.search.minEluteTime
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
468 -maxMissedCleavage $options.search.maxMissedCleavage
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
469 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
470 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
471 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
472 ## -addDecoysToBackground $options.search.addDecoysToBackground
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
473 ## -dontRunDecoys $options.search.dontRunDecoys
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
474 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
475 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
476
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
477 <xml name="options_section">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
478 <section name="options" title="Parameter Settings" expanded="false">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
479 <expand macro="common_options"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
480 <expand macro="mass_library_tolerance"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
481 <expand macro="percolator_options"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
482 <expand macro="peak_options"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
483 <expand macro="window_options"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
484 <expand macro="modification_options"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
485 <expand macro="search_options"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
486 </section>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
487 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
488
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
489 <xml name="libexport">
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
490 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
491 </xml>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
492
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
493 <token name="@SEARCH2LIB_CMDS@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
494 @CMD_IMPORTS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
495 @LINK_SCAN_INPUTS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
496 @LINK_FASTA_INPUT@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
497 @LINK_TARGET_FASTA@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
498 @LINK_LIB_INPUT@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
499 for SCAN_FILE in `ls -1 inputs/*`; do
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
500 echo "\$SCAN_FILE" &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
501 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
502 -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
503 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
504 #if not $library
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
505 -walnut
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
506 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
507 -i \$SCAN_FILE
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
508 @FASTA_INPUT@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
509 @TARGET_FASTA@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
510 @LIB_INPUT@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
511 @COMMON_OPTIONS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
512 @MASS_LIBRARY_TOLERANCE@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
513 @PERCOLATOR_OPTIONS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
514 @PEAK_OPTIONS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
515 @WINDOW_OPTIONS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
516 @MODIFICATION_OPTIONS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
517 @SEARCH_OPTIONS@ | tee -a search2lib.log
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
518 ; done &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
519 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
520 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
521 #if not $library
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
522 -pecan
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
523 #end if
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
524 @SCAN_INPUTS@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
525 @FASTA_INPUT@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
526 @TARGET_FASTA@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
527 @LIB_INPUT@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
528 -a $a
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
529 -o chromatogram_library.elib
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
530 && ls -l ./*.* inputs/*
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
531 | tee -a search2lib.log
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
532 ]]>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
533 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
534 <token name="@MSCONVERT_CMD@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
535 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
536 ]]>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
537 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
538 <token name="@MSCONVERT_RAW@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
539 mzML conversion from RAW requires special options: @MSCONVERT_CMD@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
540 ]]>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
541 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
542 <token name="@MSCONVERT_HELP@"><![CDATA[
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
543
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
544 The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
545
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
546 ::
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
547
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
548 @MSCONVERT_CMD@
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
549
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
550 ]]>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
551 </token>
4081e4faa4ab "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff changeset
552 </macros>