Mercurial > repos > galaxyp > encyclopedia_prosit_csv_to_library
annotate macros.xml @ 0:8a9cef108b0c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
author | galaxyp |
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date | Mon, 14 Sep 2020 17:06:37 +0000 |
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children | 0e25453fbee7 |
rev | line source |
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0
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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changeset
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1 <macros> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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2 <token name="@VERSION@">0.9.5</token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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3 <xml name="requirements"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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changeset
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4 <requirements> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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5 <requirement type="package" version="@VERSION@">encyclopedia</requirement> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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6 <yield/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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7 </requirements> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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8 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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9 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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10 <token name="@ENCYCLOPEDIA_WIKI@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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11 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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12 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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14 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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15 <xml name="citations"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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16 <citations> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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17 <citation type="doi">10.1038/s41467-018-07454-w</citation> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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18 <citation type="doi">10.1038/s41467-020-15346-1</citation> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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19 <citation type="doi">10.1074/mcp.P119.001913</citation> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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20 <yield/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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21 </citations> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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22 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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23 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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24 <token name="@CMD_IMPORTS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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25 #import re |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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26 #def identifier_or_name($input1) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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27 #if hasattr($input1, 'element_identifier') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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28 #return $input1.element_identifier |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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29 #else |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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30 #return $input1.name |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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31 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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32 #end def |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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33 #def clean($name1) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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34 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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35 #return $name_clean |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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36 #end def |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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37 #def ln_name($ds) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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38 #set $ext = '' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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39 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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40 #set $ext = ".mzML" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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41 #else if $ds.is_of_type('elib') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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42 #set $ext = ".elib" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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43 #else if $ds.is_of_type('dlib') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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44 #set $ext = ".dlib" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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45 #else if $ds.is_of_type('blib') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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46 #set $ext = ".blib" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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47 #else if $ds.is_of_type('fasta') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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48 #set $ext = ".fasta" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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49 #else if $ds.is_of_type('fasta.gz') |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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50 #set $ext = ".fasta.gz" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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51 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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52 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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53 #return $name |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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54 #end def |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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55 #set $i_name = None |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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56 #set $f_name = None |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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57 #set $l_name = None |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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58 #set $t_name = None |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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59 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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60 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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61 <xml name="scan_input"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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62 <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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63 <help>@MSCONVERT_RAW@</help> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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64 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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65 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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66 <token name="@LINK_SCAN_INPUT@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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67 #set $i_name = $ln_name($scan_input) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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68 ln -s '$scan_input' '$i_name' && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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69 ]]></token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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70 <token name="@SCAN_INPUT@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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71 -i '$i_name' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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72 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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73 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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74 <xml name="scan_inputs"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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75 <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
76 <help>@MSCONVERT_RAW@</help> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
77 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
78 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
80 #set $inputs_dir = 'inputs' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
81 mkdir -p $inputs_dir && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
82 #for $sf in $scan_inputs |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
83 #set $i_name = $ln_name($sf) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
84 ln -s '$sf' '${inputs_dir}/${i_name}' && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
85 #end for |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
86 ]]></token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
87 <token name="@SCAN_INPUTS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
88 -i '$inputs_dir' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
89 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
90 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
91 <xml name="fasta_input"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
92 <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
93 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
94 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
95 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
96 <token name="@LINK_FASTA_INPUT@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
97 #set $f_name = $ln_name($fasta) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
98 ln -s '$fasta' '$f_name' && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
99 ]]></token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
100 <token name="@FASTA_INPUT@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
101 -f '$f_name' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
102 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
103 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
104 <xml name="target_fasta"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
105 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
106 <help>Optional - Only analyze this subset of the background fasta proteome</help> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
107 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
108 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
109 <help>Rather than full proteins</help> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
110 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
111 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
112 <token name="@LINK_TARGET_FASTA@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
113 #if $target_fasta |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
114 #set $t_name = $ln_name($target_fasta) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
115 ln -s '$target_fasta' '$t_name' && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
116 #else |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
117 #set $t_name = None |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
118 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
119 ]]></token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
120 <token name="@TARGET_FASTA@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
121 #if $t_name |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
122 -t '$t_name' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
123 -tp $tp |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
124 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
125 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
126 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
127 <xml name="lib_input" token_optional="true" token_libhelp=""> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
128 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
129 <help>@LIBHELP@</help> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
130 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
131 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
132 <token name="@LINK_LIB_INPUT@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
133 #if $library |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
134 #set $l_name = $ln_name($library) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
135 cp '$library' '$l_name' && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
136 #else |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
137 #set $l_name = None |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
138 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
139 ]]></token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
140 <token name="@LIB_INPUT@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
141 #if $l_name |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
142 -l '$l_name' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
143 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
144 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
145 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
146 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
147 token_cid_selected="false" token_hcd_selected="false"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
148 <conditional name="acquisition"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
149 <param name="set_acquisition" type="select" label="Set Acquisition Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
150 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
151 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
152 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
153 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
154 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
155 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
156 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
157 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
158 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
159 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
160 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
161 <option value="Trypsin">Trypsin</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
162 <option value="Trypsin/p">Trypsin/p</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
163 <option value="Lys-C">Lys-C</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
164 <option value="Lys-N">Lys-N</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
165 <option value="Arg-C">Arg-C</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
166 <option value="Glu-C">Glu-C</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
167 <option value="Chymotrypsin">Chymotrypsin</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
168 <option value="Pepsin A">Pepsin A</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
169 <option value="Elastase">Elastase</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
170 <option value="Thermolysin">Thermolysin</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
171 <option value="No Enzyme">No Enzyme</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
172 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
173 <param argument="-frag" type="select" optional="true" label="Fragmentation"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
174 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
175 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
176 <option value="ETD">ETD (C/Z/Z+1)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
177 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
178 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
179 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
180 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
181 <xml name="encyclopedia_common_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
182 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
183 token_cid_selected="true" token_hcd_selected="false"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
184 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
185 <xml name="walnut_common_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
186 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
187 token_cid_selected="false" token_hcd_selected="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
188 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
189 <token name="@COMMON_OPTIONS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
190 #if $options.acquisition.set_acquisition == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
191 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
192 #if $options.acquisition.acquisition |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
193 -acquisition '$options.acquisition.acquisition' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
194 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
195 #if $options.acquisition.enzyme: |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
196 -enzyme '$options.acquisition.enzyme' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
197 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
198 #if $options.acquisition.frag: |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
199 -frag '$options.acquisition.frag' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
200 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
201 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
202 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
203 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
204 <xml name="mass_tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
205 <conditional name="tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
206 <param name="set_tolerance" type="select" label="Set Tolerance Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
207 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
208 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
209 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
210 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
211 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
212 <conditional name="precursor_tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
213 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
214 <option value="PPM">PPM</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
215 <option value="AMU">AMU</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
216 <option value="Resolution">Resolution</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
217 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
218 <when value="PPM"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
219 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
220 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
221 <when value="AMU"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
222 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
223 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
224 <when value="Resolution"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
225 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
226 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
227 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
228 <conditional name="fragment_tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
229 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
230 <option value="PPM">PPM</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
231 <option value="AMU">AMU</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
232 <option value="Resolution">Resolution</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
233 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
234 <when value="PPM"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
235 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
236 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
237 <when value="AMU"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
238 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
239 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
240 <when value="Resolution"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
241 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
242 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
243 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
244 <yield/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
245 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
246 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
247 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
248 <token name="@MASS_TOLERANCE@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
249 #if $options.tolerance.set_tolerance == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
250 -ptolunits $options.tolerance.precursor_tolerance.ptolunits |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
251 -ptol $options.tolerance.precursor_tolerance.ptol |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
252 -ftolunits $options.tolerance.fragment_tolerance.ftolunits |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
253 -ftol $options.tolerance.fragment_tolerance.ftol |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
254 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
255 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
256 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
257 <xml name="mass_library_tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
258 <expand macro="mass_tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
259 <conditional name="library_tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
260 <param argument="-ltolunits" type="select" label="Library Mass Tolerance"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
261 <option value="defaults">Use defaults</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
262 <option value="PPM">PPM</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
263 <option value="AMU">AMU</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
264 <option value="Resolution">Resolution</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
265 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
266 <when value="defaults"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
267 <when value="PPM"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
268 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
269 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
270 <when value="AMU"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
271 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
272 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
273 <when value="Resolution"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
274 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
275 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
276 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
277 </expand> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
278 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
279 <token name="@MASS_LIBRARY_TOLERANCE@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
280 @MASS_TOLERANCE@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
281 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
282 -ltolunits $options.tolerance.library_tolerance.ltolunits |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
283 -ltol $options.tolerance.library_tolerance.ltol |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
284 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
285 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
286 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
287 <xml name="percolator_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
288 <conditional name="percolator"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
289 <param name="set_percolator" type="select" label="Set Percolator Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
290 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
291 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
292 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
293 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
294 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
295 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
296 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
297 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
298 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
299 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
300 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
301 <token name="@PERCOLATOR_OPTIONS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
302 #if $options.percolator.set_percolator == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
303 #if str($options.percolator.percolatorVersionNumber) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
304 -percolatorVersionNumber $options.percolator.percolatorVersionNumber |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
305 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
306 #if str($options.percolator.percolatorProteinThreshold) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
307 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
308 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
309 #if str($options.percolator.percolatorThreshold) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
310 -percolatorThreshold $options.percolator.percolatorThreshold |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
311 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
312 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
313 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
314 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
315 <xml name="peak_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
316 <conditional name="peak"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
317 <param name="set_peak" type="select" label="Set Peak Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
318 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
319 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
320 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
321 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
322 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
323 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
324 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
325 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
326 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
327 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
328 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
329 <option value="false">No</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
330 <option value="true">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
331 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
332 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
333 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
334 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
335 <token name="@PEAK_OPTIONS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
336 #if $options.peak.set_peak == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
337 #if str($options.peak.numberOfQuantitativePeaks) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
338 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
339 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
340 #if str($options.peak.minNumOfQuantitativePeaks) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
341 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
342 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
343 #if str($options.peak.minQuantitativeIonNumber) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
344 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
345 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
346 #if str($options.peak.minIntensity) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
347 -minIntensity $options.peak.minIntensity |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
348 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
349 #if str($options.peak.expectedPeakWidth) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
350 -expectedPeakWidth $options.peak.expectedPeakWidth |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
351 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
352 #if $options.peak.filterPeaklists |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
353 -filterPeaklists $options.peak.filterPeaklists |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
354 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
355 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
356 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
357 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
358 <xml name="window_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
359 <conditional name="window"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
360 <param name="set_window" type="select" label="Set Window Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
361 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
362 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
363 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
364 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
365 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
366 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
367 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
368 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
369 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
370 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
371 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
372 <option value="window">Across entire window</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
373 <option value="recal20">Recalibrated (20% gradient)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
374 <option value="recal">Recalibrated (peak width only)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
375 <option value="uncal20">Uncalibrated (20% gradient)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
376 <option value="uncal">Uncalibrated (peak width only)</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
377 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
378 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
379 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
380 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
381 <token name="@WINDOW_OPTIONS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
382 #if $options.window.set_window == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
383 #if str($options.window.foffset) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
384 -foffset $options.window.foffset |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
385 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
386 #if str($options.window.poffset) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
387 -poffset $options.window.poffset |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
388 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
389 #if str($options.window.precursorIsolationMargin) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
390 -precursorIsolationMargin $options.window.precursorIsolationMargin |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
391 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
392 #if str($options.window.precursorWindowSize) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
393 -precursorWindowSize $options.window.precursorWindowSize |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
394 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
395 #if str($options.window.rtWindowInMin) |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
396 -rtWindowInMin $options.window.rtWindowInMin |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
397 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
398 #if $options.window.scoringBreadthType |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
399 -scoringBreadthType $options.window.scoringBreadthType |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
400 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
401 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
402 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
403 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
404 <xml name="modification_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
405 <conditional name="modifications"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
406 <param name="set_modifications" type="select" label="Set Modifications Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
407 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
408 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
409 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
410 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
411 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
412 <param argument="-fixed" type="select" optional="true" label="Fixed Modification"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
413 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
414 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
415 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
416 <option value="C=125.047679">C+125 (NEM) C=125.047679</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
417 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
418 <yield/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
419 <!-- |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
420 <param argument="-localizationModification" type="select" optional="true" label="localizationModification"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
421 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
422 --> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
423 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
424 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
425 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
426 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
427 <token name="@MODIFICATION_OPTIONS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
428 #if $options.modifications.set_modifications == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
429 #if $options.modifications.fixed |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
430 -fixed $options.modifications.fixed |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
431 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
432 -verifyModificationIons $options.modifications.verifyModificationIons |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
433 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
434 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
435 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
436 <xml name="search_options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
437 <conditional name="search"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
438 <param name="set_search" type="select" label="Set Search Options"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
439 <option value="no">No - use default options</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
440 <option value="yes">Yes</option> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
441 </param> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
442 <when value="no"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
443 <when value="yes"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
444 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
445 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
446 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
447 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
448 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
449 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
450 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
451 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
452 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
453 <!-- |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
454 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
455 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
456 --> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
457 </when> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
458 </conditional> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
459 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
460 <token name="@SEARCH_OPTIONS@"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
461 #if $options.search.set_search == 'yes' |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
462 -minCharge $options.search.minCharge |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
463 -maxCharge $options.search.maxCharge |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
464 -minLength $options.search.minLength |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
465 -maxLength $options.search.maxLength |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
466 -minEluteTime $options.search.minEluteTime |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
467 -maxMissedCleavage $options.search.maxMissedCleavage |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
468 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
469 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
470 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
471 ## -addDecoysToBackground $options.search.addDecoysToBackground |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
472 ## -dontRunDecoys $options.search.dontRunDecoys |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
473 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
474 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
475 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
476 <xml name="options_section"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
477 <section name="options" title="Parameter Settings" expanded="false"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
478 <expand macro="common_options"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
479 <expand macro="mass_library_tolerance"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
480 <expand macro="percolator_options"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
481 <expand macro="peak_options"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
482 <expand macro="window_options"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
483 <expand macro="modification_options"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
484 <expand macro="search_options"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
485 </section> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
486 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
487 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
488 <xml name="libexport"> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
489 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
490 </xml> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
491 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
492 <token name="@SEARCH2LIB_CMDS@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
493 @CMD_IMPORTS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
494 @LINK_SCAN_INPUTS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
495 @LINK_FASTA_INPUT@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
496 @LINK_TARGET_FASTA@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
497 @LINK_LIB_INPUT@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
498 for SCAN_FILE in `ls -1 inputs/*`; do |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
499 echo "\$SCAN_FILE" && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
500 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
501 -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
502 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}" |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
503 #if not $library |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
504 -walnut |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
505 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
506 -i \$SCAN_FILE |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
507 @FASTA_INPUT@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
508 @TARGET_FASTA@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
509 @LIB_INPUT@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
510 @COMMON_OPTIONS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
511 @MASS_LIBRARY_TOLERANCE@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
512 @PERCOLATOR_OPTIONS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
513 @PEAK_OPTIONS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
514 @WINDOW_OPTIONS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
515 @MODIFICATION_OPTIONS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
516 @SEARCH_OPTIONS@ | tee -a search2lib.log |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
517 ; done && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
518 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
519 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
520 #if not $library |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
521 -pecan |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
522 #end if |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
523 @SCAN_INPUTS@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
524 @FASTA_INPUT@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
525 @TARGET_FASTA@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
526 @LIB_INPUT@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
527 -a $a |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
528 -o chromatogram_library.elib |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
529 && ls -l ./*.* inputs/* |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
530 | tee -a search2lib.log |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
changeset
|
531 ]]> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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532 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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533 <token name="@MSCONVERT_CMD@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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534 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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535 ]]> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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536 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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537 <token name="@MSCONVERT_RAW@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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538 mzML conversion from RAW requires special options: @MSCONVERT_CMD@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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539 ]]> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
diff
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540 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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541 <token name="@MSCONVERT_HELP@"><![CDATA[ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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542 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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543 The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options: |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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544 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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545 :: |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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546 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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547 @MSCONVERT_CMD@ |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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548 |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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549 ]]> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
parents:
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550 </token> |
8a9cef108b0c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
galaxyp
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551 </macros> |