Mercurial > repos > jjohnson > encyclopedia_quantify
annotate macros.xml @ 1:acf6acfc8632 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
author | jjohnson |
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date | Wed, 01 Jul 2020 11:24:39 -0400 |
parents | d3a6bc607825 |
children | 174886084dc5 |
rev | line source |
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0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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1 <macros> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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2 <token name="@VERSION@">0.9.5</token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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3 <xml name="requirements"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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4 <requirements> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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5 <requirement type="package" version="@VERSION@">encyclopedia</requirement> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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6 <yield/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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7 </requirements> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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8 </xml> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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9 |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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10 <token name="@ENCYCLOPEDIA_WIKI@"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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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. |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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12 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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14 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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15 <xml name="citations"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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16 <citations> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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17 <citation type="doi">10.1038/s41467-018-07454-w</citation> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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18 <citation type="doi">10.1038/s41467-020-15346-1</citation> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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19 <citation type="doi">10.1074/mcp.P119.001913</citation> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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20 <yield/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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21 </citations> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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22 </xml> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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23 |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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24 <token name="@CMD_IMPORTS@"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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25 #import re |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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26 #def identifier_or_name($input1) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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27 #if hasattr($input1, 'element_identifier') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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28 #return $input1.element_identifier |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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29 #else |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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30 #return $input1.name |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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31 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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32 #end def |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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33 #def clean($name1) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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34 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz')))) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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35 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz'))) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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36 #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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37 #return $name_clean |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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38 #end def |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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39 #def ln_name($ds) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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40 #set $ext = '' |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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41 #if $ds.is_of_type('mzml') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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42 #set $ext = ".mzML" |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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43 #else if $ds.is_of_type('elib') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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44 #set $ext = ".elib" |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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45 #else if $ds.is_of_type('dlib') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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46 #set $ext = ".dlib" |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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47 #else if $ds.is_of_type('blib') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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48 #set $ext = ".blib" |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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49 #else if $ds.is_of_type('fasta') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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50 #set $ext = ".fasta" |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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51 #else if $ds.is_of_type('fasta.gz') |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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52 #set $ext = ".fasta.gz" |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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53 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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54 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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55 #return $name |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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56 #end def |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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57 #set $i_name = None |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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58 #set $f_name = None |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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59 #set $l_name = None |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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60 #set $t_name = None |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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61 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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62 |
d3a6bc607825
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63 <xml name="scan_input"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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64 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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65 <help>@MSCONVERT_RAW@</help> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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66 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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67 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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68 <token name="@LINK_SCAN_INPUT@"><![CDATA[ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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69 #set $i_name = $ln_name($i) |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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70 ln -s '$i' '$i_name' && |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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71 ]]></token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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72 <token name="@SCAN_INPUT@"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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73 -i '$i_name' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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74 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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75 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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76 <xml name="scan_inputs"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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77 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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78 <help>@MSCONVERT_RAW@</help> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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79 </param> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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80 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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81 <token name="@LINK_SCAN_INPUTS@"><![CDATA[ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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82 #set $inputs_dir = 'inputs' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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83 mkdir -p $inputs_dir && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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84 #for $sf in $i |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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85 #set $i_name = $ln_name($sf) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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86 ln -s '$sf' '${inputs_dir}/${i_name}' && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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87 #end for |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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88 ]]></token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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89 <token name="@SCAN_INPUTS@"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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90 -i '$inputs_dir' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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91 </token> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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92 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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93 <xml name="fasta_input"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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94 <param argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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95 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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96 </param> |
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97 </xml> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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98 <token name="@LINK_FASTA_INPUT@"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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99 #set $f_name = $ln_name($f) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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100 ln -s '$f' '$f_name' && |
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101 ]]></token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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102 <token name="@FASTA_INPUT@"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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103 -f '$f_name' |
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104 </token> |
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105 |
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106 <xml name="target_fasta"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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107 <param argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/> |
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108 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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109 </xml> |
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110 <token name="@LINK_TARGET_FASTA@"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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111 #if $t |
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112 #set $t_name = $ln_name($t) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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113 ln -s '$t' '$t_name' && |
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114 #else |
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115 #set $t_name = None |
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116 #end if |
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117 ]]></token> |
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118 <token name="@TARGET_FASTA@"> |
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119 #if $t_name |
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120 -t '$t_name' |
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121 -tp $tp |
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122 #end if |
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123 </token> |
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124 |
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125 <xml name="lib_input" token_optional="true" token_libhelp=""> |
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126 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> |
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127 <help>@LIBHELP@</help> |
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128 </param> |
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129 </xml> |
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130 <token name="@LINK_LIB_INPUT@"><![CDATA[ |
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131 #if $l |
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132 #set $l_name = $ln_name($l) |
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133 cp '$l' $l_name && |
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134 #else |
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135 #set $l_name = None |
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136 #end if |
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137 ]]></token> |
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138 <token name="@LIB_INPUT@"> |
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139 #if $l_name |
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140 -l '$l_name' |
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141 #end if |
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142 </token> |
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143 |
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144 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false" |
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145 token_cid_selected="false" token_hcd_selected="false"> |
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146 <conditional name="acquisition"> |
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147 <param name="set_acquisition" type="select" label="Set Acquisition Options"> |
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148 <option value="no">No - use default options</option> |
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149 <option value="yes">Yes</option> |
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150 </param> |
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151 <when value="no"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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152 <when value="yes"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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153 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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154 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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155 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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156 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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157 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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158 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme"> |
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159 <option value="Trypsin">Trypsin</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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160 <option value="Trypsin/p">Trypsin/p</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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161 <option value="Lys-C">Lys-C</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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162 <option value="Lys-N">Lys-N</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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163 <option value="Arg-C">Arg-C</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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164 <option value="Glu-C">Glu-C</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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165 <option value="Chymotrypsin">Chymotrypsin</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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166 <option value="Pepsin A">Pepsin A</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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167 <option value="Elastase">Elastase</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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168 <option value="Thermolysin">Thermolysin</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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169 <option value="No Enzyme">No Enzyme</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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170 </param> |
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171 <param argument="-frag" type="select" optional="true" label="Fragmentation"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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172 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option> |
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173 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option> |
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174 <option value="ETD">ETD (C/Z/Z+1)</option> |
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175 </param> |
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176 </when> |
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177 </conditional> |
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178 </xml> |
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179 <xml name="encyclopedia_common_options"> |
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180 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false" |
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181 token_cid_selected="true" token_hcd_selected="false"/> |
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182 </xml> |
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183 <xml name="walnut_common_options"> |
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184 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" |
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185 token_cid_selected="false" token_hcd_selected="true"/> |
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186 </xml> |
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187 <token name="@COMMON_OPTIONS@"> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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188 #if $options.acquisition.set_acquisition == 'yes' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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189 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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190 #if $options.acquisition.acquisition |
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191 -acquisition '$options.acquisition.acquisition' |
0
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192 #end if |
1
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193 #if $options.acquisition.enzyme: |
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194 -enzyme '$options.acquisition.enzyme' |
0
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195 #end if |
1
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196 #if $options.acquisition.frag: |
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197 -frag '$options.acquisition.frag' |
0
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198 #end if |
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199 #end if |
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200 </token> |
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201 |
d3a6bc607825
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202 <xml name="mass_tolerance"> |
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203 <conditional name="tolerance"> |
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204 <param name="set_tolerance" type="select" label="Set Tolerance Options"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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205 <option value="no">No - use default options</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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206 <option value="yes">Yes</option> |
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207 </param> |
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208 <when value="no"/> |
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209 <when value="yes"> |
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210 <conditional name="precursor_tolerance"> |
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211 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance"> |
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212 <option value="PPM">PPM</option> |
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213 <option value="AMU">AMU</option> |
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214 <option value="Resolution">Resolution</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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215 </param> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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216 <when value="PPM"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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217 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/> |
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218 </when> |
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219 <when value="AMU"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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220 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/> |
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221 </when> |
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222 <when value="Resolution"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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223 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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224 </when> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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225 </conditional> |
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226 <conditional name="fragment_tolerance"> |
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227 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance"> |
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228 <option value="PPM">PPM</option> |
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229 <option value="AMU">AMU</option> |
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230 <option value="Resolution">Resolution</option> |
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231 </param> |
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232 <when value="PPM"> |
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233 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/> |
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234 </when> |
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235 <when value="AMU"> |
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236 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/> |
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237 </when> |
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238 <when value="Resolution"> |
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239 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/> |
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240 </when> |
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241 </conditional> |
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242 <yield/> |
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243 </when> |
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244 </conditional> |
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245 </xml> |
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246 <token name="@MASS_TOLERANCE@"> |
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247 #if $options.tolerance.set_tolerance == 'yes' |
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248 -ptolunits $options.tolerance.precursor_tolerance.ptolunits |
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249 -ptol $options.tolerance.precursor_tolerance.ptol |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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250 -ftolunits $options.tolerance.fragment_tolerance.ftolunits |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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251 -ftol $options.tolerance.fragment_tolerance.ftol |
0
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252 #end if |
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253 </token> |
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254 |
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255 <xml name="mass_library_tolerance"> |
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256 <expand macro="mass_tolerance"> |
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257 <conditional name="library_tolerance"> |
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258 <param argument="-ltolunits" type="select" label="Library Mass Tolerance"> |
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259 <option value="defaults">Use defaults</option> |
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260 <option value="PPM">PPM</option> |
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261 <option value="AMU">AMU</option> |
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262 <option value="Resolution">Resolution</option> |
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263 </param> |
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264 <when value="defaults"/> |
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265 <when value="PPM"> |
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266 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/> |
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267 </when> |
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268 <when value="AMU"> |
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269 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/> |
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270 </when> |
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271 <when value="Resolution"> |
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272 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/> |
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273 </when> |
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274 </conditional> |
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275 </expand> |
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276 </xml> |
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277 <token name="@MASS_LIBRARY_TOLERANCE@"> |
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278 @MASS_TOLERANCE@ |
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279 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults' |
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280 -ltolunits $options.tolerance.library_tolerance.ltolunits |
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281 -ltol $options.tolerance.library_tolerance.ltol |
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282 #end if |
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283 </token> |
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284 |
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285 <xml name="percolator_options"> |
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286 <conditional name="percolator"> |
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287 <param name="set_percolator" type="select" label="Set Percolator Options"> |
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288 <option value="no">No - use default options</option> |
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289 <option value="yes">Yes</option> |
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290 </param> |
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291 <when value="no"/> |
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292 <when value="yes"> |
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293 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> |
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294 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> |
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295 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> |
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296 </when> |
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297 </conditional> |
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298 </xml> |
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299 <token name="@PERCOLATOR_OPTIONS@"> |
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300 #if $options.percolator.set_percolator == 'yes' |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
301 #if str($options.percolator.percolatorVersionNumber) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
302 -percolatorVersionNumber $options.percolator.percolatorVersionNumber |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
303 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
304 #if str($options.percolator.percolatorProteinThreshold) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
305 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
306 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
307 #if str($options.percolator.percolatorThreshold) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
308 -percolatorThreshold $options.percolator.percolatorThreshold |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
309 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
310 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
311 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
312 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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diff
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|
313 <xml name="peak_options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
314 <conditional name="peak"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
315 <param name="set_peak" type="select" label="Set Peak Options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
316 <option value="no">No - use default options</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
317 <option value="yes">Yes</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
318 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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diff
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|
319 <when value="no"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
320 <when value="yes"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
321 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
322 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
323 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
324 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
325 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
326 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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diff
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|
327 <option value="false">No</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
328 <option value="true">Yes</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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diff
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|
329 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
330 </when> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
331 </conditional> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
332 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
333 <token name="@PEAK_OPTIONS@"> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
334 #if $options.peak.set_peak == 'yes' |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
335 #if str($options.peak.numberOfQuantitativePeaks) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
336 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
337 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
338 #if str($options.peak.minNumOfQuantitativePeaks) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
339 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
340 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
341 #if str($options.peak.minQuantitativeIonNumber) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
342 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
343 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
344 #if str($options.peak.minIntensity) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
345 -minIntensity $options.peak.minIntensity |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
346 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
347 #if str($options.peak.expectedPeakWidth) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
348 -expectedPeakWidth $options.peak.expectedPeakWidth |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
349 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
350 #if $options.peak.filterPeaklists |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
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|
351 -filterPeaklists $options.peak.filterPeaklists |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
352 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
353 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
354 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
355 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
356 <xml name="window_options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
357 <conditional name="window"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
358 <param name="set_window" type="select" label="Set Window Options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
359 <option value="no">No - use default options</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
360 <option value="yes">Yes</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
361 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
362 <when value="no"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
363 <when value="yes"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
364 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
365 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
366 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
367 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
368 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
369 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
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|
370 <option value="window">Across entire window</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
371 <option value="recal20">Recalibrated (20% gradient)</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
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|
372 <option value="recal">Recalibrated (peak width only)</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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|
373 <option value="uncal20">Uncalibrated (20% gradient)</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
374 <option value="uncal">Uncalibrated (peak width only)</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
375 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
376 </when> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
377 </conditional> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
378 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
379 <token name="@WINDOW_OPTIONS@"> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
380 #if $options.window.set_window == 'yes' |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
381 #if str($options.window.foffset) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
382 -foffset $options.window.foffset |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
383 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
384 #if str($options.window.poffset) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
385 -poffset $options.window.poffset |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
386 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
387 #if str($options.window.precursorIsolationMargin) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
388 -precursorIsolationMargin $options.window.precursorIsolationMargin |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
389 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
390 #if str($options.window.precursorWindowSize) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
391 -precursorWindowSize $options.window.precursorWindowSize |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
392 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
393 #if str($options.window.rtWindowInMin) |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
394 -rtWindowInMin $options.window.rtWindowInMin |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
395 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
396 #if $options.window.scoringBreadthType |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
397 -scoringBreadthType $options.window.scoringBreadthType |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
398 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
399 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
400 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
401 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
402 <xml name="modification_options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
403 <conditional name="modifications"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
404 <param name="set_modifications" type="select" label="Set Modifications Options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
405 <option value="no">No - use default options</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
406 <option value="yes">Yes</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
407 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
408 <when value="no"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
409 <when value="yes"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
410 <param argument="-fixed" type="select" optional="true" label="Fixed Modification"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
411 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
412 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
413 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
414 <option value="C=125.047679">C+125 (NEM) C=125.047679</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
415 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
416 <yield/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
417 <!-- |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
418 <param argument="-localizationModification" type="select" optional="true" label="localizationModification"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
419 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
420 --> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
421 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
422 </when> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
423 </conditional> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
424 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
425 <token name="@MODIFICATION_OPTIONS@"> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
426 #if $options.modifications.set_modifications == 'yes' |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
427 #if $options.modifications.fixed |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
428 -fixed $options.modifications.fixed |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
429 #end if |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents:
0
diff
changeset
|
430 -verifyModificationIons $options.modifications.verifyModificationIons |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
431 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
432 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
433 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
434 <xml name="search_options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
435 <conditional name="search"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
436 <param name="set_search" type="select" label="Set Search Options"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
437 <option value="no">No - use default options</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
438 <option value="yes">Yes</option> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
439 </param> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
440 <when value="no"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
441 <when value="yes"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
442 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
443 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
444 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
445 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
446 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff
changeset
|
447 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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448 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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449 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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450 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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451 <!-- |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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452 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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453 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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454 --> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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455 </when> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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456 </conditional> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
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457 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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458 <token name="@SEARCH_OPTIONS@"> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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459 #if $options.search.set_search == 'yes' |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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460 -minCharge $options.search.minCharge |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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461 -maxCharge $options.search.maxCharge |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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462 -minLength $options.search.minLength |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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463 -maxLength $options.search.maxLength |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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464 -minEluteTime $options.search.minEluteTime |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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465 -maxMissedCleavage $options.search.maxMissedCleavage |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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466 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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467 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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468 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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469 ## -addDecoysToBackground $options.search.addDecoysToBackground |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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470 ## -dontRunDecoys $options.search.dontRunDecoys |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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471 #end if |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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472 </token> |
1
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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473 |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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474 <xml name="options_section"> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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475 <section name="options" title="Parameter Settings" expanded="false"> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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476 <expand macro="common_options"/> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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477 <expand macro="mass_library_tolerance"/> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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478 <expand macro="percolator_options"/> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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479 <expand macro="peak_options"/> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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480 <expand macro="window_options"/> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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481 <expand macro="modification_options"/> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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482 </section> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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483 </xml> |
acf6acfc8632
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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484 |
0
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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485 <xml name="libexport"> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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486 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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487 </xml> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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488 <token name="@MSCONVERT_CMD@"><![CDATA[ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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489 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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490 ]]> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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491 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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492 <token name="@MSCONVERT_RAW@"><![CDATA[ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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493 mzML conversion from RAW requires special options: @MSCONVERT_CMD@ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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494 ]]> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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495 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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496 <token name="@MSCONVERT_HELP@"><![CDATA[ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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497 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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498 The MSConvert command can be used to deconvolute DIA raw files. You need to use these options |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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499 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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500 :: |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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501 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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502 @MSCONVERT_CMD@ |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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503 |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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504 ]]> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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505 </token> |
d3a6bc607825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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506 </macros> |