Mercurial > repos > galaxyp > peptideshaker
annotate ident_params.xml @ 60:a6ff76e057fd draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003"
author | galaxyp |
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date | Tue, 20 Jul 2021 08:55:11 +0000 |
parents | 943a34df6047 |
children | 3ec27b4cee7c |
rev | line source |
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57
da885ca16cb2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
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1 <tool id="ident_params" |
da885ca16cb2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
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2 name="Identification Parameters" |
58
07ff622ec007
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
galaxyp
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3 version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@" |
57
da885ca16cb2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
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55
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4 profile="20.01" |
da885ca16cb2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
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5 > |
55
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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6 <description> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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7 Sets the identification parameters to be used in SearchGUI and PeptideShaker apps |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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8 </description> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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9 <macros> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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10 <import>macros_basic.xml</import> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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11 <import>macros_modifications.xml</import> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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12 </macros> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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13 <requirements> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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14 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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15 </requirements> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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16 <expand macro="stdio" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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17 <command> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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18 <![CDATA[ |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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19 #set $bin_dir = "bin" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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20 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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21 mkdir output; |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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22 cwd=`pwd`; |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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23 export HOME=\$cwd; |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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24 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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25 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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26 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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27 echo 'running Identification Parameters CLI' && |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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28 ##################################################### |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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29 ## generate IdentificationParameters for SearchGUI ## |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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30 ##################################################### |
57
da885ca16cb2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
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31 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI |
55
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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32 --exec_dir="./bin/" |
59
943a34df6047
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
galaxyp
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33 -use_log_folder 0 |
55
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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34 -out './IdentificationParametersOutput.par' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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35 ## SPECTRUM MATCHING PARAMETERS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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36 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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37 -frag_tol '${spectrum_matching_options.fragment_tol}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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38 -frag_ppm '${spectrum_matching_options.fragment_tol_units}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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39 -prec_tol '${spectrum_matching_options.precursor_ion_tol}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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40 -prec_ppm '${spectrum_matching_options.precursor_ion_tol_units}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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41 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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42 #if $spectrum_matching_options.digestion.cleavage == 'default': |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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43 -mc $spectrum_matching_options.digestion.missed_cleavages |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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44 #elif $spectrum_matching_options.digestion.cleavage == '0' and len($spectrum_matching_options.digestion.digests) > 0: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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45 #set $enzymes = [] |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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46 #set $missed_cleavages = [] |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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47 #set $specificities = [] |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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48 #for $i, $digest in enumerate($spectrum_matching_options.digestion.digests): |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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49 #silent $enzymes.append(str($digest.enzyme)) |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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50 #silent $missed_cleavages.append(str($digest.missed_cleavages)) |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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51 #silent $specificities.append(str($digest.specificity)) |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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52 #end for |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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53 -enzyme "#echo ','.join($enzymes)#" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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54 -mc "#echo ','.join($missed_cleavages)#" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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55 -specificity "#echo ','.join($specificities)#" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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56 #else: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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57 -digestion $spectrum_matching_options.digestion.cleavage |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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58 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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59 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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60 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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61 #set $fixed_mods_str = $spectrum_matching_options.fixed_modifications or '' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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62 #set $variable_mods_str = $spectrum_matching_options.variable_modifications or '' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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63 #if $fixed_mods_str |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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64 -fixed_mods "$fixed_mods_str" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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65 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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66 #if $variable_mods_str |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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67 -variable_mods "$variable_mods_str" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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68 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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69 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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70 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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71 -min_charge $spectrum_matching_options.min_charge |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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72 -max_charge $spectrum_matching_options.max_charge |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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73 -fi $spectrum_matching_options.forward_ion |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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74 -ri $spectrum_matching_options.reverse_ion |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
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75 -min_isotope ${spectrum_matching_options.min_isotope} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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76 -max_isotope ${spectrum_matching_options.max_isotope} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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77 ## TODO: TO CHECK, these last two both are also present in the app in the import filters section. |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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78 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
79 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
80 ## -- SEARCH ENGINES SPECIFIC PARAMETERS -- |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
81 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
82 ## XTANDEM ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
83 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
84 #if $searchengines_options.xtandem.xtandem_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
85 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
86 ## Spectrum import |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
87 #if $searchengines_options.xtandem.xtandem_spectrum.xtandem_spectrum_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
88 -xtandem_dynamic_range ${searchengines_options.xtandem.xtandem_spectrum.xtandem_dynamic_range} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
89 -xtandem_npeaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_npeaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
90 -xtandem_min_frag_mz ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_frag_mz} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
91 -xtandem_min_peaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_peaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
92 -xtandem_noise_suppr ${searchengines_options.xtandem.xtandem_spectrum.xtandem_noise_suppr} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
93 -xtandem_min_prec_mass ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
94 -xtandem_parent_isotope_correction ${searchengines_options.xtandem.xtandem_spectrum.xtandem_parent_isotope_correction} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
95 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
96 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
97 ## Advanced search |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
98 #if $searchengines_options.xtandem.xtandem_asearch.xtandem_asearch_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
99 -xtandem_quick_acetyl ${searchengines_options.xtandem.xtandem_asearch.xtandem_quick_acetyl} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
100 -xtandem_quick_pyro ${searchengines_options.xtandem.xtandem_asearch.xtandem_quick_pyro} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
101 -xtandem_stp_bias ${searchengines_options.xtandem.xtandem_asearch.xtandem_stp_bias} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
102 -xtandem_ptm_complexity ${searchengines_options.xtandem.xtandem_asearch.xtandem_ptm_complexity} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
103 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
104 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
105 ## Output |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
106 #if $searchengines_options.xtandem.xtandem_output.xtandem_output_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
107 -xtandem_output_results $searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_output_results_selector |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
108 #if $searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_output_results_selector != "all" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
109 -xtandem_evalue ${searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_evalue} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
110 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
111 -xtandem_output_proteins ${searchengines_options.xtandem.xtandem_output.xtandem_output_proteins} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
112 -xtandem_output_sequences ${searchengines_options.xtandem.xtandem_output.xtandem_output_sequences} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
113 -xtandem_output_spectra ${searchengines_options.xtandem.xtandem_output.xtandem_output_spectra} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
114 -xtandem_output_histograms ${searchengines_options.xtandem.xtandem_output.xtandem_output_histograms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
115 ## TODO: Integration with Skyline not ready yet: -xtandem_skyline_path ${searchengines_options.xtandem.xtandem_output.xtandem_skyline_path} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
116 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
117 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
118 ## Refinement |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
119 #if $searchengines_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
120 -xtandem_refine 1 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
121 -xtandem_refine_evalue ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_evalue} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
122 -xtandem_refine_unc ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_unc} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
123 -xtandem_refine_semi ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_semi} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
124 -xtandem_refine_pot ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_pot} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
125 -xtandem_refine_p_mut ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_p_mut} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
126 -xtandem_refine_snaps ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_snaps} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
127 -xtandem_refine_spec_synt ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_spec_synt} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
128 #else |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
129 -xtandem_refine 0 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
130 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
131 #else |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
132 -xtandem_output_spectra 1 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
133 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
134 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
135 ## MYRIMATCH ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
136 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
137 #if $searchengines_options.myrimatch.myrimatch_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
138 -myrimatch_min_pep_length ${searchengines_options.myrimatch.myrimatch_min_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
139 -myrimatch_max_pep_length ${searchengines_options.myrimatch.myrimatch_max_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
140 -myrimatch_min_prec_mass ${searchengines_options.myrimatch.myrimatch_min_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
141 -myrimatch_max_prec_mass ${searchengines_options.myrimatch.myrimatch_max_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
142 -myrimatch_num_matches ${searchengines_options.myrimatch.myrimatch_num_matches} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
143 -myrimatch_num_ptms ${searchengines_options.myrimatch.myrimatch_num_ptms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
144 -myrimatch_fragmentation ${searchengines_options.myrimatch.myrimatch_fragmentation} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
145 -myrimatch_termini ${searchengines_options.myrimatch.myrimatch_termini} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
146 -myrimatch_plus_three ${searchengines_options.myrimatch.myrimatch_plus_three} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
147 -myrimatch_xcorr ${searchengines_options.myrimatch.myrimatch_xcorr} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
148 -myrimatch_tic_cutoff ${searchengines_options.myrimatch.myrimatch_tic_cutoff} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
149 -myrimatch_intensity_classes ${searchengines_options.myrimatch.myrimatch_intensity_classes} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
150 -myrimatch_class_multiplier ${searchengines_options.myrimatch.myrimatch_class_multiplier} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
151 -myrimatch_num_batches ${searchengines_options.myrimatch.myrimatch_num_batches} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
152 -myrimatch_max_peak ${searchengines_options.myrimatch.myrimatch_max_peak} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
153 -myrimatch_output ${searchengines_options.myrimatch.myrimatch_output} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
154 #else |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
155 -myrimatch_output mzIdentML |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
156 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
157 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
158 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
159 ## MSGF+ ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
160 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
161 #if $searchengines_options.msgf.msgf_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
162 -msgf_decoy ${searchengines_options.msgf.msgf_decoy} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
163 -msgf_instrument ${searchengines_options.msgf.msgf_instrument} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
164 -msgf_fragmentation ${searchengines_options.msgf.msgf_fragmentation} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
165 -msgf_protocol ${searchengines_options.msgf.msgf_protocol} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
166 -msgf_termini ${searchengines_options.msgf.msgf_termini} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
167 -msgf_min_pep_length ${searchengines_options.msgf.msgf_min_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
168 -msgf_max_pep_length ${searchengines_options.msgf.msgf_max_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
169 -msgf_num_ptms ${searchengines_options.msgf.msgf_num_ptms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
170 -msgf_num_matches ${searchengines_options.msgf.msgf_num_matches} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
171 -msgf_additional ${searchengines_options.msgf.msgf_additional} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
172 #if $searchengines_options.msgf.msgf_tasks.msgf_tasks_custom == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
173 -msgf_num_tasks ${searchengines_options.msgf.msgf_tasks.msgf_num_tasks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
174 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
175 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
176 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
177 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
178 ## MSAMANDA ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
179 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
180 #if $searchengines_options.ms_amanda.ms_amanda_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
181 -ms_amanda_decoy ${searchengines_options.ms_amanda.ms_amanda_decoy} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
182 -ms_amanda_instrument "${searchengines_options.ms_amanda.ms_amanda_instrument}" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
183 -ms_amanda_max_rank ${searchengines_options.ms_amanda.ms_amanda_max_rank} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
184 -ms_amanda_mono ${searchengines_options.ms_amanda.ms_amanda_mono} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
185 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
186 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
187 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
188 ## ANDROMEDA ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
189 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
190 #* Not working in tests |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
191 #if $searchengines_options.andromeda.andromeda_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
192 -andromeda_max_pep_mass ${searchengines_options.andromeda.andromeda_max_pep_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
193 -andromeda_max_comb ${searchengines_options.andromeda.andromeda_max_comb} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
194 -andromeda_top_peaks ${searchengines_options.andromeda.andromeda_top_peaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
195 -andromeda_top_peaks_window ${searchengines_options.andromeda.andromeda_top_peaks_window} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
196 -andromeda_incl_water ${searchengines_options.andromeda.andromeda_incl_water} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
197 -andromeda_incl_ammonia ${searchengines_options.andromeda.andromeda_incl_ammonia} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
198 -andromeda_neutral_losses ${searchengines_options.andromeda.andromeda_neutral_losses} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
199 -andromeda_fragment_all ${searchengines_options.andromeda.andromeda_fragment_all} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
200 -andromeda_emp_correction ${searchengines_options.andromeda.andromeda_emp_correction} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
201 -andromeda_higher_charge ${searchengines_options.andromeda.andromeda_higher_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
202 -andromeda_equal_il ${searchengines_options.andromeda.andromeda_equal_il} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
203 -andromeda_frag_method ${searchengines_options.andromeda.andromeda_frag_method} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
204 -andromeda_max_mods ${searchengines_options.andromeda.andromeda_max_mods} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
205 -andromeda_min_pep_length ${searchengines_options.andromeda.andromeda_min_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
206 -andromeda_max_pep_length ${searchengines_options.andromeda.andromeda_max_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
207 -andromeda_max_psms ${searchengines_options.andromeda.andromeda_max_psms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
208 -andromeda_decoy_mode ${searchengines_options.andromeda.andromeda_decoy_mode} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
209 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
210 *# |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
211 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
212 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
213 ## OMSSA ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
214 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
215 #if $searchengines_options.omssa.omssa_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
216 ## Spectrum |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
217 #if $searchengines_options.omssa.omssa_spectrum.omssa_spectrum_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
218 -omssa_low_intensity "${searchengines_options.omssa.omssa_spectrum.omssa_low_intensity}" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
219 -omssa_high_intensity ${searchengines_options.omssa.omssa_spectrum.omssa_high_intensity} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
220 -omssa_intensity_incr ${searchengines_options.omssa.omssa_spectrum.omssa_intensity_incr} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
221 -omssa_min_peaks ${searchengines_options.omssa.omssa_spectrum.omssa_min_peaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
222 -omssa_remove_prec ${searchengines_options.omssa.omssa_spectrum.omssa_remove_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
223 -omssa_estimate_charge ${searchengines_options.omssa.omssa_spectrum.omssa_estimate_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
224 -omssa_plus_one ${searchengines_options.omssa.omssa_spectrum.omssa_plus_one} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
225 -omssa_fraction ${searchengines_options.omssa.omssa_spectrum.omssa_fraction} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
226 -omssa_prec_per_spectrum ${searchengines_options.omssa.omssa_spectrum.omssa_prec_per_spectrum} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
227 -omssa_scale_prec ${searchengines_options.omssa.omssa_spectrum.omssa_scale_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
228 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
229 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
230 ## Spectrum |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
231 #if $searchengines_options.omssa.omssa_database.omssa_database_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
232 -omssa_memory ${searchengines_options.omssa.omssa_database.omssa_memory} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
233 -omssa_methionine ${searchengines_options.omssa.omssa_database.omssa_methionine} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
234 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
235 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
236 ## Database |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
237 #if $searchengines_options.omssa.omssa_search.omssa_search_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
238 -omssa_neutron ${searchengines_options.omssa.omssa_search.omssa_neutron} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
239 -omssa_single_window_wd ${searchengines_options.omssa.omssa_search.omssa_single_window_wd} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
240 -omssa_double_window_wd ${searchengines_options.omssa.omssa_search.omssa_double_window_wd} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
241 -omssa_single_window_pk ${searchengines_options.omssa.omssa_search.omssa_single_window_pk} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
242 -omssa_double_window_pk ${searchengines_options.omssa.omssa_search.omssa_double_window_pk} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
243 -omssa_min_ann_int_pks ${searchengines_options.omssa.omssa_search.omssa_min_ann_int_pks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
244 -omssa_min_annotated_peaks ${searchengines_options.omssa.omssa_search.omssa_min_annotated_peaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
245 -omssa_max_ladders ${searchengines_options.omssa.omssa_search.omssa_max_ladders} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
246 -omssa_max_frag_charge ${searchengines_options.omssa.omssa_search.omssa_max_frag_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
247 -omssa_charge ${searchengines_options.omssa.omssa_search.omssa_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
248 -omssa_forward ${searchengines_options.omssa.omssa_search.omssa_forward} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
249 -omssa_rewind ${searchengines_options.omssa.omssa_search.omssa_rewind} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
250 -omssa_max_frag_series ${searchengines_options.omssa.omssa_search.omssa_max_frag_series} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
251 -omssa_corr ${searchengines_options.omssa.omssa_search.omssa_corr} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
252 -omssa_consecutive_p ${searchengines_options.omssa.omssa_search.omssa_consecutive_p} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
253 -omssa_hitlist_charge ${searchengines_options.omssa.omssa_search.omssa_hitlist_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
254 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
255 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
256 ## Iterative Search |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
257 #if $searchengines_options.omssa.omssa_isearch.omssa_isearch_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
258 -omssa_it_sequence_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_sequence_evalue} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
259 -omssa_it_spectrum_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_spectrum_evalue} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
260 -omssa_it_replace_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_replace_evalue} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
261 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
262 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
263 ## Semi-enzymatic |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
264 #if $searchengines_options.omssa.omssa_senzymatic.omssa_senzymatic_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
265 -omssa_min_pep_length ${searchengines_options.omssa.omssa_senzymatic.omssa_min_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
266 -omssa_max_pep_length ${searchengines_options.omssa.omssa_senzymatic.omssa_max_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
267 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
268 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
269 ## Output |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
270 #if $searchengines_options.omssa.omssa_output_conditional.omssa_output_conditional_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
271 -omssa_max_evalue ${searchengines_options.omssa.omssa_output_conditional.omssa_max_evalue} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
272 -omssa_hitlist_length ${searchengines_options.omssa.omssa_output_conditional.omssa_hitlist_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
273 -omssa_format ${searchengines_options.omssa.omssa_output_conditional.omssa_format} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
274 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
275 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
276 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
277 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
278 ## COMET ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
279 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
280 #if $searchengines_options.comet.comet_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
281 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
282 #if $searchengines_options.comet.comet_spectrum.comet_spectrum_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
283 -comet_min_peaks ${searchengines_options.comet.comet_spectrum.comet_min_peaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
284 -comet_min_peak_int ${searchengines_options.comet.comet_spectrum.comet_min_peak_int} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
285 -comet_remove_prec ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
286 #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
287 -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
288 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
289 #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
290 -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
291 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
292 #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "3" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
293 -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
294 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
295 -comet_clear_mz_range_lower ${searchengines_options.comet.comet_spectrum.comet_clear_mz_range_lower} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
296 -comet_clear_mz_range_upper ${searchengines_options.comet.comet_spectrum.comet_clear_mz_range_upper} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
297 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
298 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
299 #if $searchengines_options.comet.comet_search.comet_search_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
300 -comet_enzyme_type ${searchengines_options.comet.comet_search.comet_enzyme_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
301 -comet_isotope_correction ${searchengines_options.comet.comet_search.comet_isotope_correction} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
302 -comet_min_prec_mass ${searchengines_options.comet.comet_search.comet_min_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
303 -comet_max_prec_mass ${searchengines_options.comet.comet_search.comet_max_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
304 -comet_max_frag_charge ${searchengines_options.comet.comet_search.comet_max_frag_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
305 -comet_remove_meth ${searchengines_options.comet.comet_search.comet_remove_meth} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
306 -comet_batch_size ${searchengines_options.comet.comet_search.comet_batch_size} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
307 -comet_num_ptms ${searchengines_options.comet.comet_search.comet_num_ptms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
308 -comet_req_ptms ${searchengines_options.comet.comet_search.comet_req_ptms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
309 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
310 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
311 #if $searchengines_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
312 -comet_theoretical_fragment_ions ${searchengines_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
313 -comet_frag_bin_offset ${searchengines_options.comet.comet_fragment_ions.comet_frag_bin_offset} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
314 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
315 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
316 #if $searchengines_options.comet.comet_output.comet_output_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
317 -comet_num_matches ${searchengines_options.comet.comet_output.comet_num_matches} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
318 -comet_output ${searchengines_options.comet.comet_output.comet_output_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
319 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
320 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
321 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
322 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
323 ## TIDE ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
324 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
325 #if $searchengines_options.tide.tide_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
326 ## Index parameters |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
327 #if $searchengines_options.tide.tide_index.tide_index_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
328 -tide_min_pep_length ${searchengines_options.tide.tide_index.tide_min_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
329 -tide_max_pep_length ${searchengines_options.tide.tide_index.tide_max_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
330 -tide_min_prec_mass ${searchengines_options.tide.tide_index.tide_min_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
331 -tide_max_prec_mass ${searchengines_options.tide.tide_index.tide_max_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
332 -tide_monoisotopic ${searchengines_options.tide.tide_index.tide_monoisotopic} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
333 -tide_clip_n_term ${searchengines_options.tide.tide_index.tide_clip_n_term} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
334 #if str($searchengines_options.tide.tide_index.tide_num_ptms).strip() != '': |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
335 -tide_num_ptms ${searchengines_options.tide.tide_index.tide_num_ptms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
336 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
337 -tide_num_ptms_per_type ${searchengines_options.tide.tide_index.tide_num_ptms_per_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
338 -tide_digestion_type ${searchengines_options.tide.tide_index.tide_digestion_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
339 -tide_print_peptides ${searchengines_options.tide.tide_index.tide_print_peptides} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
340 -tide_decoy_format ${searchengines_options.tide.tide_index.tide_decoy_format} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
341 -tide_keep_terminals ${searchengines_options.tide.tide_index.tide_keep_terminals} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
342 -tide_decoy_seed ${searchengines_options.tide.tide_index.tide_decoy_seed} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
343 -tide_remove_temp ${searchengines_options.tide.tide_index.tide_remove_temp} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
344 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
345 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
346 ## Search parameters |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
347 #if $searchengines_options.tide.tide_search.tide_search_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
348 -tide_compute_p ${searchengines_options.tide.tide_search.tide_compute_p} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
349 -tide_compute_sp ${searchengines_options.tide.tide_search.tide_compute_sp} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
350 -tide_min_spectrum_mz ${searchengines_options.tide.tide_search.tide_min_spectrum_mz} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
351 #if str($searchengines_options.tide.tide_search.tide_max_spectrum_mz).strip() != '': |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
352 -tide_max_spectrum_mz ${searchengines_options.tide.tide_search.tide_max_spectrum_mz} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
353 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
354 -tide_min_spectrum_peaks ${searchengines_options.tide.tide_search.tide_min_spectrum_peaks} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
355 -tide_spectrum_charges ${searchengines_options.tide.tide_search.tide_spectrum_charges} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
356 -tide_remove_prec ${searchengines_options.tide.tide_search.tide_remove_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
357 -tide_remove_prec_tol ${searchengines_options.tide.tide_search.tide_remove_prec_tol} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
358 -tide_use_flanking ${searchengines_options.tide.tide_search.tide_use_flanking} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
359 -tide_use_neutral_losses ${searchengines_options.tide.tide_search.tide_use_neutral_losses} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
360 -tide_mz_bin_width ${searchengines_options.tide.tide_search.tide_mz_bin_width} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
361 -tide_mz_bin_offset ${searchengines_options.tide.tide_search.tide_mz_bin_offset} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
362 -tide_max_psms ${searchengines_options.tide.tide_search.tide_max_psms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
363 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
364 #set $format_list = str($searchengines_options.tide.tide_search.tide_export).split(',') |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
365 #set $formats_available = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"] |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
366 #for $format_available in $formats_available: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
367 #if $format_available in $format_list: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
368 -$format_available 1 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
369 #else: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
370 -$format_available 0 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
371 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
372 #end for |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
373 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
374 -tide_output_folder ${searchengines_options.tide.tide_output_folder} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
375 -tide_verbosity ${searchengines_options.tide.tide_verbosity} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
376 -tide_progress_indicator ${searchengines_options.tide.tide_progress_indicator} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
377 -tide_concat ${searchengines_options.tide.tide_concat} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
378 #if str($searchengines_options.tide.tide_store_spectra).strip() != '': |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
379 -tide_store_spectra ${searchengines_options.tide.tide_store_spectra} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
380 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
381 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
382 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
383 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
384 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
385 ## DIRECTTAG ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
386 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
387 #if $searchengines_options.directtag.directtag_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
388 -directag_tag_length ${searchengines_options.directtag.directag_tag_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
389 -directag_max_var_mods ${searchengines_options.directtag.directag_max_var_mods} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
390 -directag_charge_states ${searchengines_options.directtag.directag_charge_states} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
391 -directag_duplicate_spectra ${searchengines_options.directtag.directag_duplicate_spectra} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
392 -directag_isotope_tolerance ${searchengines_options.directtag.directag_isotope_tolerance} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
393 -directag_deisotoping ${searchengines_options.directtag.directag_deisotoping} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
394 -directag_intensity_classes ${searchengines_options.directtag.directag_intensity_classes} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
395 #if str($searchengines_options.directtag.directag_output_suffix).strip() != '': |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
396 -directag_output_suffix ${searchengines_options.directtag.directag_output_suffix} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
397 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
398 -directag_max_peak_count ${searchengines_options.directtag.directag_max_peak_count} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
399 -directag_max_tag_count ${searchengines_options.directtag.directag_max_tag_count} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
400 -directag_tic_cutoff ${searchengines_options.directtag.directag_tic_cutoff} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
401 -directag_complement_tolerance ${searchengines_options.directtag.directag_complement_tolerance} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
402 -directag_adjustment_step ${searchengines_options.directtag.directag_adjustment_step} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
403 -directag_min_adjustment ${searchengines_options.directtag.directag_min_adjustment} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
404 -directag_max_adjustment ${searchengines_options.directtag.directag_max_adjustment} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
405 -directag_intensity_weight ${searchengines_options.directtag.directag_intensity_weight} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
406 -directag_fidelity_weight ${searchengines_options.directtag.directag_fidelity_weight} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
407 -directag_complement_weight ${searchengines_options.directtag.directag_complement_weight} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
408 -directag_adjust_precursor ${searchengines_options.directtag.directag_adjust_precursor} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
409 -directag_ms_charge_state ${searchengines_options.directtag.directag_ms_charge_state} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
410 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
411 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
412 ## METAMORPHEUS ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
413 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
414 #if $searchengines_options.metamorpheus.metamorpheus_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
415 ## Search options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
416 #if $searchengines_options.metamorpheus.metamorpheus_search.metamorpheus_search_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
417 -meta_morpheus_search_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_search_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
418 -meta_morpheus_num_partitions ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_num_partitions} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
419 -meta_morpheus_dissociation_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_dissociation_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
420 -meta_morpheus_max_mods_for_peptide ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_max_mods_for_peptide} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
421 -meta_morpheus_score_cutoff ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_score_cutoff} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
422 -meta_morpheus_use_delta_score ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_use_delta_score} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
423 -meta_morpheus_mass_diff_acceptor_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_mass_diff_acceptor_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
424 -meta_morpheus_min_pep_length ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_min_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
425 -meta_morpheus_max_pep_length ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_max_pep_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
426 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
427 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
428 ## Output options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
429 #if $searchengines_options.metamorpheus.metamorpheus_output.metamorpheus_output_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
430 -meta_morpheus_write_mzid ${searchengines_options.metamorpheus.metamorpheus_output.meta_morpheus_write_mzid} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
431 -meta_morpheus_write_pepxml ${searchengines_options.metamorpheus.metamorpheus_output.meta_morpheus_write_pepxml} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
432 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
433 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
434 ## Deisotoping options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
435 #if $searchengines_options.metamorpheus.metamorpheus_deisotoping.metamorpheus_deisotoping_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
436 -meta_morpheus_use_provided_prec ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_use_provided_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
437 -meta_morpheus_do_prec_deconv ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_do_prec_deconv} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
438 -meta_morpheus_deconv_int_ratio ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_int_ratio} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
439 -meta_morpheus_deconv_mass_tol ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_mass_tol} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
440 -meta_morpheus_deconv_mass_tol_type ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_mass_tol_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
441 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
442 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
443 ## Protein grouping options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
444 #if $searchengines_options.metamorpheus.metamorpheus_proteingrouping.metamorpheus_proteingrouping_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
445 -meta_morpheus_mod_peptides_are_different ${searchengines_options.metamorpheus.metamorpheus_proteingrouping.meta_morpheus_mod_peptides_are_different} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
446 -meta_morpheus_no_one_hit_wonders ${searchengines_options.metamorpheus.metamorpheus_proteingrouping.meta_morpheus_no_one_hit_wonders} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
447 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
448 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
449 ## Peak trimming options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
450 #if $searchengines_options.metamorpheus.metamorpheus_peaktrimming.metamorpheus_peaktrimming_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
451 -meta_morpheus_trim_ms1 ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_trim_ms1} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
452 -meta_morpheus_trim_msms ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_trim_msms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
453 -meta_morpheus_num_peaks_per_window ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_num_peaks_per_window} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
454 -meta_morpheus_min_allowed_int_ratio_to_base_peak ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_min_allowed_int_ratio_to_base_peak} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
455 -meta_morpheus_window_with_thompson ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_window_with_thompson} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
456 -meta_morpheus_num_windows ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_num_windows} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
457 -meta_morpheus_norm_across_all_windows ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_norm_across_all_windows} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
458 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
459 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
460 ## Silico digestion related options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
461 #if $searchengines_options.metamorpheus.metamorpheus_silico.metamorpheus_silico_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
462 -meta_morpheus_frag_term ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_frag_term} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
463 -meta_morpheus_max_frag_size ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_max_frag_size} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
464 -meta_morpheus_search_target ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_search_target} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
465 -meta_morpheus_decoy_type ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_decoy_type} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
466 -meta_morpheus_max_mod_isoforms ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_max_mod_isoforms} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
467 -meta_morpheus_min_variant_depth ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_min_variant_depth} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
468 -meta_morpheus_min_variant_depth ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_min_variant_depth} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
469 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
470 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
471 ## G-PTM search related options |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
472 #if $searchengines_options.metamorpheus.metamorpheus_gptm.metamorpheus_gptm_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
473 -meta_morpheus_gptm ${searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
474 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
475 ## Need to transform the list of gptm acronyms to real gptm values for SearchGUI |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
476 #if str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories) != "None" and str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories) != "" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
477 #set $meta_morpheus_gptm_categories_list = set(str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories).split(',')) |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
478 #else |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
479 #set $meta_morpheus_gptm_categories_list = set() |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
480 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
481 #set $meta_morpheus_categories_mapping = {'common_fixed_variable': 'Common Fixed and Variable', 'common_biological': 'Common Biological','common_artifact': 'Common Artifact', 'metal': 'Metal','less_common': 'Less Common','labeling': 'Labeling','subs_1n': 'Substitution (1 Nucleotide)','subs_2n': 'Substitution (2+ Nucleotides)','other': 'Other'} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
482 #set $meta_morpheus_gptm_real_categories_list = [] |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
483 #for $meta_morpheus_gptm_category_item in $meta_morpheus_gptm_categories_list: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
484 $meta_morpheus_gptm_real_categories_list.append("'"+$meta_morpheus_categories_mapping[$meta_morpheus_gptm_category_item]+"'") |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
485 #end for |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
486 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
487 #if len($meta_morpheus_gptm_real_categories_list) > 0 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
488 -meta_morpheus_gptm_categories #echo ','.join($meta_morpheus_gptm_real_categories_list)# |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
489 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
490 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
491 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
492 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
493 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
494 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
495 ## NOVOR ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
496 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
497 #if $searchengines_options.novor.novor_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
498 -novor_fragmentation ${searchengines_options.novor.novor_fragmentation} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
499 -novor_mass_analyzer ${searchengines_options.novor.novor_mass_analyzer} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
500 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
501 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
502 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
503 ## PEPNOVO+ ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
504 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
505 #if $searchengines_options.pepnovo.pepnovo_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
506 -pepnovo_hitlist_length ${searchengines_options.pepnovo.pepnovo_hitlist_length} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
507 -pepnovo_estimate_charge ${searchengines_options.pepnovo.pepnovo_estimate_charge} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
508 -pepnovo_correct_prec_mass ${searchengines_options.pepnovo.pepnovo_correct_prec_mass} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
509 -pepnovo_discard_spectra ${searchengines_options.pepnovo.pepnovo_discard_spectra} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
510 -pepnovo_generate_blast ${searchengines_options.pepnovo.pepnovo_generate_blast} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
511 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
512 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
513 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
514 ## PNOVO+ ADVANCED SETTINGS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
515 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
516 #if $searchengines_options.pnovo.pnovo_advanced == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
517 -pnovo_num_peptides ${searchengines_options.pnovo.pnovo_num_peptides} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
518 -pnovo_lower_prec ${searchengines_options.pnovo.pnovo_lower_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
519 -pnovo_upper_prec ${searchengines_options.pnovo.pnovo_upper_prec} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
520 -pnovo_activation ${searchengines_options.pnovo.pnovo_activation} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
521 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
522 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
523 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
524 ## -- ADVANCED PARAMETERS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
525 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
526 ## SPECTRUM ANNOTATION |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
527 -annotation_level $advanced_options.spectrum_annotation_options.annotation_level |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
528 -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
529 -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
530 ## TODO: There are still many options from the GUI to be incorporated to the CLI |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
531 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
532 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
533 ## SEQUENCE MATCHING |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
534 -sequence_matching_type $advanced_options.sequence_matching_options.sequence_matching_type |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
535 -sequence_matching_x $advanced_options.sequence_matching_options.sequence_matching_x |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
536 -sequence_matching_enzymatic_tags $advanced_options.sequence_matching_options.sequence_matching_enzymatic_tags |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
537 -sequence_matching_max_ptms_per_tag $advanced_options.sequence_matching_options.sequence_matching_max_ptms_per_tag |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
538 -sequence_matching_min_amino_acid_score $advanced_options.sequence_matching_options.sequence_matching_min_amino_acid_score |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
539 -sequence_matching_min_tag_length $advanced_options.sequence_matching_options.sequence_matching_min_tag_length |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
540 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
541 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
542 ## IMPORT FILTERS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
543 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
544 -import_peptide_length_min '${advanced_options.import_filters_options.min_peptide_length}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
545 -import_peptide_length_max '${advanced_options.import_filters_options.max_peptide_length}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
546 -import_precursor_mz '${advanced_options.import_filters_options.max_precursor_error}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
547 -import_precursor_mz_ppm '${advanced_options.import_filters_options.max_precursor_error_type}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
548 #if $advanced_options.import_filters_options.missed_cleavages_min |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
549 -import_missed_cleavages_min '${advanced_options.import_filters_options.missed_cleavages_min}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
550 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
551 #if $advanced_options.import_filters_options.missed_cleavages_max |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
552 -import_missed_cleavages_max '${advanced_options.import_filters_options.missed_cleavages_max}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
553 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
554 -exclude_unknown_ptms '${advanced_options.import_filters_options.exclude_unknown_ptms}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
555 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
556 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
557 ## PTM LOCALIZATION |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
558 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
559 -ptm_score '${advanced_options.ptm_localization_options.ptm_score.ptm_score_selector}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
560 #if $advanced_options.ptm_localization_options.ptm_score.ptm_score_selector == 1 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
561 -score_neutral_losses '${advanced_options.ptm_localization_options.ptm_score.neutral_losses}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
562 #if str($advanced_options.ptm_localization_options.ptm_score.ptm_threshold) != '' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
563 -ptm_threshold '${advanced_options.ptm_localization_options.ptm_score.ptm_threshold}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
564 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
565 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
566 -ptm_alignment '${advanced_options.ptm_localization_options.ptm_alignment}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
567 -ptm_sequence_matching_type '${advanced_options.ptm_localization_options.ptm_sequence_matching_type}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
568 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
569 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
570 ## GENE ANNOTATION |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
571 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
572 $advanced_options.gene_annotation_options.use_gene_mapping |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
573 #if $advanced_options.gene_annotation_options.use_gene_mapping: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
574 $advanced_options.gene_annotation_options.update_gene_mapping |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
575 #else: |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
576 -updateGeneMapping 0 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
577 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
578 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
579 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
580 ## PROTEIN INFERENCE |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
581 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
582 #if $advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
583 -simplify_groups 1 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
584 -simplify_evidence ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_evidence} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
585 -simplify_confidence ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_confidence} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
586 -simplify_confidence_threshold ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_confidence_threshold} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
587 -simplify_enzymaticity ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_enzymaticity} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
588 -simplify_variant ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_variant} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
589 #else |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
590 -simplify_groups 0 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
591 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
592 -pi_modifications ${advanced_options.protein_inference_options.simplify_protein_pi_modifications} |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
593 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
594 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
595 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
596 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
597 ## VALIDATION LEVELS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
598 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
599 -protein_fdr '${advanced_options.validation_levels_options.protein_fdr}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
600 -peptide_fdr '${advanced_options.validation_levels_options.peptide_fdr}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
601 -psm_fdr '${advanced_options.validation_levels_options.psm_fdr}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
602 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
603 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
604 ## FRACTION ANALYSIS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
605 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
606 -protein_fraction_mw_confidence '${advanced_options.fraction_analysis_options.protein_fraction_mw_confidence}' |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
607 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
608 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
609 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
610 ## DATABASE PROCESSING OPTIONS |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
611 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
612 #if $advanced_options.database_processing_options.decoy_conditional.create_decoy_selector == "yes" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
613 -fasta_target_decoy 1 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
614 -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
615 -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
616 #end if |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
617 -fasta_target_decoy 0 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
618 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
619 ]]> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
620 </command> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
621 <inputs> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
622 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
623 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
624 <!-- SPECTRUM MATCHING PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
625 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
626 <section name="spectrum_matching_options" expanded="false" title="Spectrum Matching Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
627 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
628 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
629 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
630 <expand macro="modifications"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
631 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
632 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
633 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
634 <expand macro="modifications"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
635 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
636 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
637 <conditional name="digestion"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
638 <param name="cleavage" type="select" label="Digestion"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
639 <option value="0">Select Enzymes</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
640 <option value="1">Unspecific Cleavage</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
641 <option value="2">Whole Protein</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
642 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
643 <when value="0"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
644 <repeat name="digests" min="1" title="Enzymes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
645 <param name="enzyme" type="select" label="Enzyme" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
646 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
647 <option value="Trypsin">Trypsin</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
648 <option value="Trypsin (no P rule)">Trypsin (no P rule)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
649 <option value="Arg-C">Arg-C</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
650 <option value="Arg-C (no P rule)">Arg-C</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
651 <option value="Arg-N">Arg-N</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
652 <option value="Glu-C">Glu-C</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
653 <option value="Lys-C">Lys-C</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
654 <option value="Lys-C (no P rule)">Lys-C (no P rule)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
655 <option value="Lys-N">Lys-N</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
656 <option value="Asp-N">Asp-N</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
657 <option value="Asp-N (ambic)">Asp-N (ambic)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
658 <option value="Chymotrypsin">Chymotrypsin</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
659 <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
660 <option value="Pepsin A">Pepsin A</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
661 <option value="CNBr">CNBr</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
662 <option value="Thermolysin">Thermolysin</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
663 <option value="LysargiNase">LysargiNase</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
664 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
665 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
666 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
667 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
668 <param name="specificity" type="select" label="Specificity"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
669 <option value="0" selected="true">Specific at both termini</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
670 <option value="1">Semi-Specific - one terminus</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
671 <option value="2">Specific at the N-terminus only</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
672 <option value="3">Specific at the C-terminus only</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
673 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
674 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
675 </repeat> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
676 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
677 <when value="1"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
678 <when value="2"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
679 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
680 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
681 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
682 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
683 <option value="1">Parts per million (ppm)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
684 <option value="0">Daltons</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
685 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
686 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
687 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
688 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
689 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
690 <option value="1">Parts per million (ppm)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
691 <option value="0" selected="true">Daltons</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
692 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
693 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
694 help="Provide error value for fragment ions, based on instrument used"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
695 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
696 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
697 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
698 <option value="a">a</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
699 <option value="b" selected="true">b</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
700 <option value="c">c</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
701 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
702 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
703 <option value="x">x</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
704 <option value="y" selected="true">y</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
705 <option value="z">z</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
706 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
707 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
708 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
709 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
710 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
711 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
712 <!-- - SEARCH ENGINES OPTIONS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
713 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
714 <section name="searchengines_options" expanded="false" title="Search Engines Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
715 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
716 <!-- X!TANDEM ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
717 <conditional name="xtandem"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
718 <param name="xtandem_advanced" type="select" label="X!Tandem Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
719 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
720 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
721 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
722 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
723 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
724 <!-- Spectrum Import --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
725 <conditional name="xtandem_spectrum"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
726 <param name="xtandem_spectrum_selector" type="select" label="X!Tandem: Spectrum Import Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
727 <option value="yes" selected="True">Set Spectrum Import Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
728 <option value="no">Keep Default Spectrum Import Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
729 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
730 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
731 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
732 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
733 label="X!Tandem: Dynamic Range" value="100" type="integer" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
734 <param name="xtandem_npeaks" type="integer" value="50" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
735 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
736 <param name="xtandem_min_frag_mz" type="integer" value="200" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
737 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
738 <param name="xtandem_min_peaks" type="integer" value="5" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
739 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
740 <param name="xtandem_noise_suppr" type="boolean" checked="false" truevalue="1" falsevalue="0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
741 label="X!Tandem: Noise Suppression" help="Use noise suppression"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
742 <param name="xtandem_min_prec_mass" type="integer" value="500" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
743 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
744 <param name="xtandem_parent_isotope_correction" type="boolean" checked="true" truevalue="1" falsevalue="0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
745 label="X!Tandem: Parent monoisotopic mass isotope error" help="when activated, the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide. "/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
746 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
747 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
748 <!-- Advanced search --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
749 <conditional name="xtandem_asearch"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
750 <param name="xtandem_asearch_selector" type="select" label="X!Tandem: Advanced Search Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
751 <option value="yes">Set Advanced Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
752 <option value="no" selected="True">Keep Default Advanced Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
753 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
754 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
755 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
756 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
757 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
758 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
759 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
760 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
761 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
762 <param name="xtandem_ptm_complexity" type="float" value="6.0" help="maximum number of variable modification alternatives that will be tested for a particular peptide" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
763 label="X!Tandem: PTM complexity" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
764 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
765 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
766 <!-- Output --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
767 <conditional name="xtandem_output"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
768 <param name="xtandem_output_selector" type="select" label="X!Tandem: Output Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
769 <option value="yes">Set Output Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
770 <option value="no" selected="True">Keep Default Output Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
771 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
772 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
773 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
774 <conditional name="xtandem_output_results_conditional"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
775 <param name="xtandem_output_results_selector" type="select" label="" help="Determines which results are written to the output file at the end of a modelling session"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
776 <option value="all" selected="True">All</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
777 <option value="valid" >Valid</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
778 <option value="stochastic" >Stochastic</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
779 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
780 <when value="all"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
781 <when value="valid"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
782 <param name="xtandem_evalue" help="Highest value for recorded peptides" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
783 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
784 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
785 <when value="stochastic"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
786 <param name="xtandem_evalue" help="Highest value for recorded peptides" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
787 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
788 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
789 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
790 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
791 <param name="xtandem_output_proteins" help="Controls output of protein sequences" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
792 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
793 <param name="xtandem_output_sequences" help="Controls output of sequence information" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
794 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
795 <param name="xtandem_output_spectra" help="Controls output of spectrum information" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
796 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
797 <param name="xtandem_output_histograms" help="Controls output of statistical information about an spectrum-to-sequence assignment" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
798 label="X!Tandem: Output Histograms" type="boolean" truevalue="1" falsevalue="0" checked="false" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
799 <!-- TODO: Integration with Skyline not ready yet |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
800 <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
801 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
802 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
803 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
804 <!-- Refine --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
805 <conditional name="xtandem_refine"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
806 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
807 <option value="no">Don't refine</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
808 <option value="yes" selected="True">Use refinement</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
809 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
810 <when value="no"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
811 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
812 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
813 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
814 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
815 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
816 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
817 label="X!Tandem: semi-enzymatic cleavage, refinement" help="Search for semi-tryptic peptides during refinement"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
818 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
819 label="X!Tandem: Use potential modifications for full refinement" help="Controls the use of refinement modifications in all refinement modules."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
820 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
821 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
822 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
823 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
824 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
825 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
826 <!-- TODO: Refinement modifications when implemented in the command line --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
827 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
828 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
829 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
830 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
831 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
832 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
833 <!-- MyriMatch ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
834 <conditional name="myrimatch"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
835 <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
836 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
837 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
838 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
839 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
840 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
841 <param name="myrimatch_min_pep_length" type="integer" value="6" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
842 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
843 <param name="myrimatch_max_pep_length" type="integer" value="30" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
844 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
845 <param name="myrimatch_min_prec_mass" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
846 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
847 <param name="myrimatch_max_prec_mass" type="float" value="5000.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
848 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
849 <param name="myrimatch_num_matches" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
850 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
851 <param name="myrimatch_num_ptms" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
852 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
853 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
854 <!-- TODO : TO BE UPDATED WHEN CLI DOES. TO CONFIRM MANUAL OPTION FIRSTLY --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
855 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
856 <option value="CID" selected="True">CID</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
857 <option value="HCD" >HCD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
858 <option value="ETD" >ETD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
859 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
860 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
861 <option value="0">non-tryptic</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
862 <option value="1">semi-tryptic</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
863 <option value="2" selected="True" >fully-tryptic</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
864 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
865 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
866 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
867 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
868 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
869 <param name="myrimatch_tic_cutoff" type="float" value="0.98" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
870 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
871 <param name="myrimatch_intensity_classes" type="integer" value="3" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
872 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
873 <param name="myrimatch_class_multiplier" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
874 label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
875 <param name="myrimatch_num_batches" type="integer" value="50" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
876 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
877 <param name="myrimatch_max_peak" type="integer" value="100" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
878 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
879 <param name="myrimatch_output" type="select" label="MyriMatch: output format option"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
880 <option value="mzIdentML" selected="True" >mzIdentML</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
881 <option value="pepXML">pepXML</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
882 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
883 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
884 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
885 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
886 <!-- MS-GF+ ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
887 <conditional name="msgf"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
888 <param name="msgf_advanced" type="select" label="MSGF Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
889 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
890 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
891 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
892 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
893 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
894 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
895 label="MSGF: Search Decoy Database" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
896 <param name="msgf_instrument" label="MSGF: MS/MS Detector" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
897 <option value="0" >Low-res LCQ/LTQ</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
898 <option value="1" >Orbitrap/FTICR</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
899 <option value="2" >TOF</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
900 <option value="3" selected="True">Q-Exactive</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
901 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
902 <param name="msgf_fragmentation" label="MSGF: Fragmentation method" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
903 <option value="0" >As written in the spectrum or CID if no info</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
904 <option value="1" >CID</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
905 <option value="2" >ETD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
906 <option value="3" selected="True">HCD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
907 <option value="4" >UVPD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
908 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
909 <param name="msgf_protocol" label="MSGF: Protocol" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
910 <option value="0" selected="True">Automatic</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
911 <option value="1" >Phosphorylation</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
912 <option value="2" >iTRAQ</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
913 <option value="3" >iTRAQPhospho</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
914 <option value="4" >TMT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
915 <option value="5" >Standard</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
916 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
917 <param name="msgf_termini" type="select" format="txt" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
918 label="MSGF: Enzymatic Terminals" help="Searches will take much longer if selecting a value other than 2"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
919 <option value="0">None required</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
920 <option value="1">At least one</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
921 <option value="2" selected="true">Both</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
922 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
923 <param name="msgf_min_pep_length" type="integer" value="8" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
924 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
925 <param name="msgf_max_pep_length" type="integer" value="30" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
926 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
927 <param name="msgf_num_ptms" label="MSGF: Max Variable PTMs per Peptide" type="integer" value="2"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
928 <param name="msgf_num_matches" label="MSGF: Number of Spectrum Matches" type="integer" value="10" help="Number of peptide matches per spectrum to report" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
929 <param name="msgf_additional" label="MS-GF+ additional Output" type="select" help="Additional features to export"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
930 <option value="0" selected="True">output basic scores only</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
931 <option value="1" >output additional features</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
932 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
933 <conditional name="msgf_tasks"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
934 <param name="msgf_tasks_custom" type="select" label="Number of tasks to use on the threads"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
935 <option value="yes">Custom</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
936 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
937 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
938 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
939 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
940 <param name="msgf_num_tasks" type="integer" value="4" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
941 label="MSGF: Custom number of tasks to use on the threads" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
942 help="Manually set the number of tasks to create for the search. More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). Check the documentation carefully. "/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
943 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
944 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
945 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
946 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
947 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
948 <!-- MS-AMANDA ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
949 <conditional name="ms_amanda"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
950 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
951 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
952 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
953 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
954 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
955 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
956 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
957 label="MS Amanda: Generate Decoys" help="generate decoys" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
958 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
959 help="MS Amanda instrument id option. Available ion types are listed here."> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
960 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
961 <option value="b, y" selected="True">b, y</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
962 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
963 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
964 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
965 <option value="a, b, y" >a, b, y</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
966 <option value="a, b, y, Imm" >a, b, y, Imm</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
967 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
968 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
969 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
970 <option value="b, y, INT" >b, y, INT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
971 <option value="b, y, INT, Imm" >b, y, INT, Imm</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
972 <option value="a, b, y, INT" >a, b, y, INT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
973 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
974 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
975 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
976 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
977 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
978 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
979 <param name="ms_amanda_max_rank" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
980 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
981 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
982 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
983 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
984 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
985 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
986 <!-- OMSSA ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
987 <conditional name="omssa"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
988 <param name="omssa_advanced" type="select" label="OMSSA Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
989 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
990 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
991 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
992 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
993 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
994 <!-- Spectrum --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
995 <conditional name="omssa_spectrum"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
996 <param name="omssa_spectrum_selector" type="select" label="OMSSA: Spectrum Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
997 <option value="yes" selected="True">Set Spectrum Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
998 <option value="no">Keep Default Spectrum Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
999 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1000 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1001 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1002 <param name="omssa_low_intensity" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1003 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1004 <param name="omssa_high_intensity" type="float" value="0.2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1005 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1006 <param name="omssa_intensity_incr" type="float" value="0.0005" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1007 label="OMSSA: Intensity Increment" help="Intensity increment" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1008 <param name="omssa_min_peaks" type="integer" value="4" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1009 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1010 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1011 label="OMSSA: Remove precursors" help="Eliminate charge reduced precursors in spectra" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1012 <param name="omssa_estimate_charge" type="select" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1013 label="OMSSA: Estimate charge" help="estimate precursor charge" > |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1014 <option value="0" >Believe input file</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1015 <option value="1" selected="True">Use range</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1016 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1017 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1018 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1019 <param name="omssa_fraction" type="float" value="0.95" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1020 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1021 <param name="omssa_prec_per_spectrum" type="integer" value="1" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1022 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1023 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1024 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1025 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1026 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1027 <!-- Database --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1028 <conditional name="omssa_database"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1029 <param name="omssa_database_selector" type="select" label="OMSSA: Database Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1030 <option value="yes" >Set Database Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1031 <option value="no" selected="True">Keep Default Database Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1032 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1033 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1034 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1035 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1036 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1037 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1038 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1039 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1040 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1041 <!-- Search --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1042 <conditional name="omssa_search"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1043 <param name="omssa_search_selector" type="select" label="OMSSA: Search Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1044 <option value="yes">Set Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1045 <option value="no" selected="True">Keep Default Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1046 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1047 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1048 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1049 <!-- TODO: TO BE IMPLEMENTED IN THE CLI, MINIMUM PRECURSOR CHARGE FOR MULTIPLY CHARGED FRAGMENTS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1050 <param name="omssa_neutron" type="float" value="1446.94" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1051 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1052 <param name="omssa_single_window_wd" type="integer" value="27" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1053 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1054 <param name="omssa_double_window_wd" type="integer" value="14" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1055 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1056 <param name="omssa_single_window_pk" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1057 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1058 <param name="omssa_double_window_pk" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1059 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1060 <param name="omssa_min_ann_int_pks" type="integer" value="6" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1061 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1062 <param name="omssa_min_annotated_peaks" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1063 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1064 <param name="omssa_max_ladders" type="integer" value="128" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1065 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1066 <param name="omssa_max_frag_charge" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1067 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1068 <param name="omssa_charge" type="select" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1069 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" > |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1070 <option value="0" >Minus</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1071 <option value="1" selected="True">Plus</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1072 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1073 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1074 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1075 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1076 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1077 <param name="omssa_max_frag_series" type="integer" value="100" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1078 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1079 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1080 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1081 <param name="omssa_consecutive_p" type="float" value="0.5" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1082 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1083 <param name="omssa_hitlist_charge" type="integer" value="30" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1084 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1085 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1086 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1087 <!-- Iterative Search --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1088 <conditional name="omssa_isearch"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1089 <param name="omssa_isearch_selector" type="select" label="OMSSA: Iterative Search Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1090 <option value="yes" >Set Iterative Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1091 <option value="no" selected="True">Keep Default Iterative Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1092 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1093 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1094 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1095 <param name="omssa_it_sequence_evalue" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1096 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1097 <param name="omssa_it_spectrum_evalue" type="float" value="0.01" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1098 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1099 <param name="omssa_it_replace_evalue" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1100 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search (0.0 means all)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1101 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1102 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1103 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1104 <!-- Semi-enzymatic --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1105 <conditional name="omssa_senzymatic"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1106 <param name="omssa_senzymatic_selector" type="select" label="OMSSA: Semi-enzymatic Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1107 <option value="yes" >Set Semi-enzymatic Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1108 <option value="no" selected="True">Keep Default Semi-enzymatic Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1109 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1110 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1111 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1112 <param name="omssa_min_pep_length" type="integer" value="8" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1113 label="OMSSA: Minimum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1114 <param name="omssa_max_pep_length" type="integer" value="30" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1115 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1116 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1117 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1118 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1119 <!-- Output --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1120 <conditional name="omssa_output_conditional"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1121 <param name="omssa_output_conditional_selector" type="select" label="OMSSA: Output Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1122 <option value="yes">Set Output Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1123 <option value="no" selected="True">Keep Default Output Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1124 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1125 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1126 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1127 <param name="omssa_max_evalue" type="float" value="100" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1128 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1129 <param name="omssa_hitlist_length" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1130 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1131 <param name="omssa_format" label="OMSSA output format" type="select" > |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1132 <option value="0" selected="True">OMX</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1133 <option value="1" >CSV</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1134 <option value="2" >pepXML</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1135 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1136 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1137 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1138 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1139 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1140 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1141 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1142 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1143 <!-- Comet ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1144 <conditional name="comet"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1145 <param name="comet_advanced" type="select" label="Comet Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1146 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1147 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1148 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1149 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1150 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1151 <!-- Spectrum Related parameters --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1152 <conditional name="comet_spectrum"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1153 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1154 <option value="yes" selected="True">Set Spectrum Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1155 <option value="no">Keep Default Spectrum Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1156 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1157 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1158 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1159 <param name="comet_min_peaks" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1160 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1161 <param name="comet_min_peak_int" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1162 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1163 <conditional name="comet_prec"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1164 <param name="comet_remove_prec" label="Comet: Remove Precursor peaks" type="select" help="Select for precursor m/z signal removal"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1165 <option value="0" selected="True" >no</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1166 <option value="1">yes</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1167 <option value="2">yes + charge reduced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1168 <option value="3">yes + phospate neutral</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1169 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1170 <when value="0" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1171 <when value="1"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1172 <param name="comet_remove_prec_tol" type="float" value="1.5" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1173 label="Comet: Remove Precursor Tolerance" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1174 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1175 <when value="2"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1176 <param name="comet_remove_prec_tol" type="float" value="1.5" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1177 label="Comet: Remove Precursor Tolerance" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1178 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1179 <when value="3"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1180 <param name="comet_remove_prec_tol" type="float" value="1.5" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1181 label="Comet: Remove Precursor Tolerance" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1182 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1183 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1184 <param name="comet_clear_mz_range_lower" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1185 label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1186 <param name="comet_clear_mz_range_upper" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1187 label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1188 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1189 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1190 <!-- Search Related parameters --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1191 <conditional name="comet_search"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1192 <param name="comet_search_selector" type="select" label="Comet: Search Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1193 <option value="yes">Set Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1194 <option value="no" selected="True">Keep Default Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1195 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1196 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1197 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1198 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1199 <option value="1">semi-specific</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1200 <option value="2" selected="True">full-enzyme</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1201 <option value="8">unspecific N-term</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1202 <option value="9">unspecific C-term</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1203 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1204 <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1205 <option value="0">off</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1206 <option value="1" selected="True">0,+1</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1207 <option value="2">0,+1,+2</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1208 <option value="3">0,+1,+2,+3</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1209 <option value="4">-8,-4,0,+4,+8</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1210 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1211 <param name="comet_min_prec_mass" type="float" value="600.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1212 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1213 <param name="comet_max_prec_mass" type="float" value="5000.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1214 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1215 <param name="comet_max_frag_charge" type="integer" value="3" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1216 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1217 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1218 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1219 <param name="comet_batch_size" type="integer" value="0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1220 label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1221 <param name="comet_num_ptms" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1222 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1223 <param name="comet_req_ptms" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1224 label="Comet: Require Variable PTMs" help="Require at least one variable PTM per peptide" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1225 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1226 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1227 <!-- Fragment Ions Related parameters --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1228 <conditional name="comet_fragment_ions"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1229 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1230 <option value="yes">Set Fragment Ions Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1231 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1232 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1233 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1234 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1235 <param name="comet_theoretical_fragment_ions" type="select" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1236 label="Comet: Correlation Score type" help="Specifies how theoretical fragment ion peaks are represented (on the sum in the bin alone or using flanking bins too)"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1237 <option value="0" selected="True">Summed intensities + flanking</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1238 <option value="1">Summed intensities</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1239 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1240 <param name="comet_frag_bin_offset" type="float" value="0.01" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1241 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1242 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1243 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1244 <!-- Output Related parameters --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1245 <conditional name="comet_output"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1246 <param name="comet_output_selector" type="select" label="Comet: Output Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1247 <option value="yes">Set Output Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1248 <option value="no" selected="True">Keep Default Output Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1249 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1250 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1251 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1252 <param name="comet_num_matches" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1253 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1254 <param name="comet_output_type" type="select" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1255 label="Comet: Output type" help="Output type: PepXML, SQT, TXT or Percolator"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1256 <option value="PepXML" selected="True">PepXML</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1257 <option value="SQT">SQT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1258 <option value="TXT">TXT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1259 <option value="Percolator">Percolator</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1260 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1261 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1262 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1263 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1264 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1265 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1266 <!-- TIDE ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1267 <conditional name="tide"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1268 <param name="tide_advanced" type="select" label="TIDE Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1269 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1270 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1271 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1272 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1273 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1274 <!-- Index parameters --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1275 <conditional name="tide_index"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1276 <param name="tide_index_selector" type="select" label="Tide: Index Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1277 <option value="yes" selected="True">Set Index Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1278 <option value="no" >Keep Default Index Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1279 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1280 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1281 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1282 <param name="tide_min_pep_length" type="integer" value="6" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1283 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1284 <param name="tide_max_pep_length" type="integer" value="30" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1285 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1286 <param name="tide_min_prec_mass" type="float" value="200.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1287 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1288 <param name="tide_max_prec_mass" type="float" value="7200.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1289 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1290 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1291 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1292 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1293 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1294 <param name="tide_num_ptms" type="integer" value="" optional="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1295 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1296 <param name="tide_num_ptms_per_type" type="integer" value="2" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1297 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1298 <param name="tide_digestion_type" label="TIDE: Enzyme/Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1299 <option value="full-digest" selected="True">full-digest</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1300 <option value="partial-digest" >partial-digest</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1301 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1302 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1303 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1304 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1305 <option value="none" selected="True">none</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1306 <option value="shuffle" >shuffle</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1307 <option value="peptide-revers" >peptide-reverse</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1308 <option value="protein-reverse" >protein-reverse</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1309 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1310 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1311 <option value="N" >N</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1312 <option value="C" >C</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1313 <option value="NC" selected="True">NC</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1314 <option value="non" >none</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1315 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1316 <param name="tide_decoy_seed" type="integer" value="1" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1317 label="TIDE: Decoy Seed" help="Set the decoy seed"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1318 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1319 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1320 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1321 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1322 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1323 <!-- Search parameters --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1324 <conditional name="tide_search"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1325 <param name="tide_search_selector" type="select" label="Tide: Search Related"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1326 <option value="yes">Set Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1327 <option value="no" selected="True">Keep Default Search Parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1328 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1329 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1330 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1331 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1332 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1333 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1334 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1335 <param name="tide_min_spectrum_mz" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1336 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1337 <param name="tide_max_spectrum_mz" type="float" value="" optional="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1338 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1339 <param name="tide_min_spectrum_peaks" type="integer" value="20" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1340 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1341 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1342 <option value="1" >1</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1343 <option value="2" >2</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1344 <option value="3" >3</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1345 <option value="all" selected="True">all</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1346 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1347 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1348 label="TIDE: Remove Precursor Peak" help="If true, the peak that corresponds to the precursor mass is excluded"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1349 <param name="tide_remove_prec_tol" type="float" value="1.5" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1350 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1351 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1352 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1353 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1354 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1355 <param name="tide_mz_bin_width" type="float" value="0.02" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1356 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1357 <param name="tide_mz_bin_offset" type="float" value="0.0" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1358 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1359 <param name="tide_max_psms" type="integer" value="10" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1360 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1361 <param name="tide_export" label="TIDE: Output Format" type="select" multiple="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1362 display="checkboxes" help="Choose the output format"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1363 <option value="tide_export_text" selected="True">Text</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1364 <option value="tide_export_sqt" >SQT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1365 <option value="tide_export_pepxml" >pepxml</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1366 <option value="tide_export_mzid" >MzIdentML</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1367 <option value="tide_export_pin" >Percolator input file</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1368 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1369 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1370 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1371 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1372 <!-- other options --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1373 <param name="tide_output_folder" type="text" value="crux-output" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1374 label="TIDE: Output Folder" help="Tide output folder (relative to the Tide working folder). Not to be changed if the .par file will be used by SearchGUI in Galaxy"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1375 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1376 <option value="0" >0</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1377 <option value="10" >10</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1378 <option value="20" >20</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1379 <option value="30" selected="True">30</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1380 <option value="40" >40</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1381 <option value="50" >50</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1382 <option value="60" >60</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1383 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1384 <param name="tide_progress_indicator" type="integer" value="1000" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1385 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1386 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1387 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1388 <param name="tide_store_spectra" type="text" value="" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1389 label="TIDE: Store spectra" help="Tide file name in with to store the binary spectra. Not to be changed if the .par file will be used by SearchGUI in Galaxy"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1390 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1391 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1392 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1393 <!-- Andromeda ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1394 <!-- Windows only |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1395 <conditional name="andromeda"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1396 <param name="andromeda_advanced" type="select" label="Andromeda Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1397 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1398 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1399 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1400 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1401 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1402 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1403 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1404 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1405 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1406 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1407 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1408 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1409 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1410 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1411 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1412 <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1413 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1414 <option value="CID" selected="true">CID</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1415 <option value="HCD">HCD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1416 <option value="EDT">EDT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1417 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1418 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1419 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1420 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1421 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1422 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1423 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1424 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1425 --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1426 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1427 <!-- DIRECTAG ADVANDED PARAMETERS--> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1428 <conditional name="directtag"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1429 <param name="directtag_advanced" type="select" label="DirectTag Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1430 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1431 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1432 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1433 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1434 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1435 <param name="directag_tag_length" type="integer" value="4" label="DirecTag tag length"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1436 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1437 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1438 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1439 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1440 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1441 <option value="0" selected="true">no deisotoping</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1442 <option value="1">precursor only</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1443 <option value="2">precursor and candidate</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1444 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1445 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1446 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1447 <param name="directag_max_peak_count" type="integer" value="100" label="DirecTag max peak count"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1448 <param name="directag_max_tag_count" type="integer" value="10" label="DirecTag maximum tag count"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1449 <param name="directag_tic_cutoff" type="integer" value="100" label="DirecTag TIC cutoff in percent"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1450 <validator type="in_range" min="0" max="100" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1451 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1452 <param name="directag_complement_tolerance" type="float" value="0.1" label="DirecTag complement mz tolerance"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1453 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1454 <param name="directag_min_adjustment" type="float" value="-0.5" label="DirecTag minimum precursor adjustment"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1455 <param name="directag_max_adjustment" type="float" value="1.5" label="DirecTag maximum precursor adjustment"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1456 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1457 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1458 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1459 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1460 <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag use charge state from M spectrum"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1461 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1462 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1463 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1464 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1465 <!-- METAMORPHEUS ADVANDED PARAMETERS--> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1466 <conditional name="metamorpheus"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1467 <param name="metamorpheus_advanced" type="select" label="MetaMorpheus Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1468 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1469 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1470 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1471 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1472 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1473 <conditional name="metamorpheus_search"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1474 <param name="metamorpheus_search_selector" type="select" label="MetaMorpheus: Search related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1475 <option value="yes" selected="True">Set Search parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1476 <option value="no">Keep Default Search parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1477 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1478 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1479 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1480 <param name="meta_morpheus_search_type" type="select" label="MetaMorpheus search type"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1481 <option value="Classic" selected="true">Classic</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1482 <option value="Modern">Modern</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1483 <option value="NonSpecific">NonSpecific</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1484 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1485 <param name="meta_morpheus_num_partitions" type="integer" value="1" label="MetaMorpheus number of partitions when indexing"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1486 <param name="meta_morpheus_dissociation_type" type="select" label="MetaMorpheus dissociation type"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1487 <option value="HCD" selected="true">HCD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1488 <option value="CID">CID</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1489 <option value="ECD">ECD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1490 <option value="ETD">ETD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1491 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1492 <param name="meta_morpheus_max_mods_for_peptide" type="integer" value="2" label="MetaMorpheus maximum modifications per peptide"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1493 <param name="meta_morpheus_meth" type="select" label="MetaMorpheus initiator methionine behavior"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1494 <option value="Undefined" >Undefined</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1495 <option value="Retain">Retain</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1496 <option value="Cleave">Cleave</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1497 <option value="Variable" selected="true">Variable</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1498 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1499 <param name="meta_morpheus_score_cutoff" type="float" value="5.0" label="MetaMorpheus score cutoff"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1500 <param name="meta_morpheus_use_delta_score" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus use delta score"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1501 <param name="meta_morpheus_mass_diff_acceptor_type" type="select" label="MetaMorpheus mass difference acceptor type"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1502 <option value="Exact">Exact</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1503 <option value="OneMM" selected="true">OneMM</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1504 <option value="TwoMM">TwoMM</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1505 <option value="ThreeMM" >ThreeMM</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1506 <option value="PlusOrMinusThreeMM">PlusOrMinusThreeMM</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1507 <option value="ModOpen">ModOpen</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1508 <option value="Open">Open</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1509 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1510 <param name="meta_morpheus_min_pep_length" type="integer" value="8" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1511 label="MetaMorpheus minimum peptide length" help="Minimum length for a peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1512 <param name="meta_morpheus_max_pep_length" type="integer" value="30" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1513 label="MetaMorpheus maximum peptide length" help="Maximum length for a peptide to be considered"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1514 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1515 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1516 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1517 <conditional name="metamorpheus_output"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1518 <param name="metamorpheus_output_selector" type="select" label="MetaMorpheus: Output related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1519 <option value="yes" >Set Output parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1520 <option value="no" selected="True">Keep Default Output parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1521 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1522 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1523 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1524 <param name="meta_morpheus_write_mzid" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus write mzid"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1525 <param name="meta_morpheus_write_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus write pepxml"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1526 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1527 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1528 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1529 <conditional name="metamorpheus_deisotoping"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1530 <param name="metamorpheus_deisotoping_selector" type="select" label="MetaMorpheus: Deisotoing related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1531 <option value="yes" >Set Deisotoping parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1532 <option value="no" selected="True">Keep Default Deisotoping parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1533 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1534 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1535 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1536 <param name="meta_morpheus_use_provided_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus use provided precursor info"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1537 <param name="meta_morpheus_do_prec_deconv" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus do precursor deconvolution"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1538 <param name="meta_morpheus_deconv_int_ratio" type="float" value="3.0" label="MetaMorpheus deconvolution intensity ratio"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1539 <param name="meta_morpheus_deconv_mass_tol" type="float" value="4.0" label="MetaMorpheus score cutoff"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1540 <param name="meta_morpheus_deconv_mass_tol_type" type="select" label="MetaMorpheus deoconvolution mass tolerance type"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1541 <option value="PPM" selected="true">PPM</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1542 <option value="Absolute">Absolute</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1543 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1544 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1545 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1546 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1547 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1548 <conditional name="metamorpheus_proteingrouping"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1549 <param name="metamorpheus_proteingrouping_selector" type="select" label="MetaMorpheus: Protein grouping related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1550 <option value="yes" >Set Protein grouping parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1551 <option value="no" selected="True">Keep Default Protein grouping parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1552 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1553 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1554 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1555 <param name="meta_morpheus_mod_peptides_are_different" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus modified peptides are different"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1556 <param name="meta_morpheus_no_one_hit_wonders" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus exclude one hit wonders"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1557 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1558 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1559 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1560 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1561 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1562 <conditional name="metamorpheus_peaktrimming"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1563 <param name="metamorpheus_peaktrimming_selector" type="select" label="MetaMorpheus: Peak trimming related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1564 <option value="yes" >Set Peak trimming parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1565 <option value="no" selected="True">Keep Default Peak trimming parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1566 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1567 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1568 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1569 <param name="meta_morpheus_trim_ms1" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus trim MS1 peaks"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1570 <param name="meta_morpheus_trim_msms" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus trim MSMS peaks"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1571 <param name="meta_morpheus_num_peaks_per_window" type="integer" value="200" label="MetaMorpheus number of peaks per window" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1572 <param name="meta_morpheus_min_allowed_int_ratio_to_base_peak" type="float" value="0.01" label="MetaMorpheus minimum allowed intensity ratio to base peak"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1573 <param name="meta_morpheus_window_with_thompson" type="integer" optional="true" label="MetaMorpheus window width in Thompson" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1574 <param name="meta_morpheus_num_windows" type="integer" optional="true" label="MetaMorpheus number of windows" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1575 <param name="meta_morpheus_norm_across_all_windows" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus normalize peaks across all windows"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1576 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1577 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1578 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1579 <conditional name="metamorpheus_silico"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1580 <param name="metamorpheus_silico_selector" type="select" label="MetaMorpheus: Silico digestion related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1581 <option value="yes" >Set Silico digestion parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1582 <option value="no" selected="True">Keep Default Silico digestion parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1583 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1584 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1585 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1586 <param name="meta_morpheus_frag_term" type="select" label="MetaMorpheus fragmentation terminus"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1587 <option value="Both" selected="true">Both</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1588 <option value="N">N</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1589 <option value="C">C</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1590 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1591 <param name="meta_morpheus_max_frag_size" type="float" value="30000.0" label="MetaMorpheus maximum fragmentation size"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1592 <param name="meta_morpheus_search_target" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus search target sequences"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1593 <param name="meta_morpheus_decoy_type" type="select" label="MetaMorpheus decoy type"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1594 <option value="None" selected="true">None</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1595 <option value="Reverse">Reverse</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1596 <option value="Slide">Slide</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1597 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1598 <param name="meta_morpheus_max_mod_isoforms" type="integer" value="1024" label="MetaMorpheus maximum modified isoforms" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1599 <param name="meta_morpheus_min_variant_depth" type="integer" value="1" label="MetaMorpheus minimum variant depth" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1600 <param name="meta_morpheus_max_hetrozygous_var" type="integer" value="4" label="MetaMorpheus maximum hetrozygous variants" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1601 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1602 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1603 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1604 <conditional name="metamorpheus_gptm"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1605 <param name="metamorpheus_gptm_selector" type="select" label="MetaMorpheus: G-PTM search related options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1606 <option value="yes" >Set G-PTM search parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1607 <option value="no" selected="True">Keep Default G-PTM search parameters</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1608 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1609 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1610 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1611 <param name="meta_morpheus_gptm" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus run G-PTM"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1612 <param name="meta_morpheus_gptm_categories" type="select" display="checkboxes" multiple="True" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1613 label="MetaMorpheus G-PTM categories to include in the G-PTM search"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1614 <option value="common_fixed_variable" >Common Fixed and Variable</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1615 <option value="common_biological" selected="true">Common Biological</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1616 <option value="common_artifact" selected="true">Common Artifact</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1617 <option value="metal" selected="true">Metal</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1618 <option value="less_common">Less Common</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1619 <option value="labeling">Labeling</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1620 <option value="subs_1n">Substitution (1 Nucleotide)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1621 <option value="subs_2n">Substitution (2+ Nucleotides)</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1622 <option value="other">Other</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1623 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1624 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1625 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1626 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1627 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1628 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1629 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1630 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1631 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1632 <!-- NOVOR ADVANDED PARAMETERS--> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1633 <conditional name="novor"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1634 <param name="novor_advanced" type="select" label="Novor Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1635 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1636 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1637 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1638 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1639 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1640 <param name="novor_fragmentation" type="select" label="Novor fragmentation method"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1641 <option value="HCD" selected="True">HCD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1642 <option value="CID">CID</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1643 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1644 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1645 <option value="Trap" >Trap</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1646 <option value="TOF" >TOF</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1647 <option value="FT" selected="True">FT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1648 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1649 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1650 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1651 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1652 <!-- PEPNOVO+ ADVANDED PARAMETERS--> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1653 <conditional name="pepnovo"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1654 <param name="pepnovo_advanced" type="select" label="PepNovo+ Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1655 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1656 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1657 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1658 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1659 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1660 <param name="pepnovo_hitlist_length" type="integer" value="10" label="PepNovo+ number of de novo solutions [0-2000], default is '10'."> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1661 <validator type="in_range" min="0" max="2000" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1662 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1663 <param name="pepnovo_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ estimate precursor charge option."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1664 <param name="pepnovo_correct_prec_mass" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ correct precursor mass option."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1665 <param name="pepnovo_discard_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ discard low quality spectra option."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1666 <param name="pepnovo_generate_blast" type="boolean" truevalue="1" falsevalue="0" checked="false" label="PepNovo+ generate a BLAST query."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1667 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1668 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1669 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1670 <!-- PNOVO+ ADVANDED PARAMETERS--> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1671 <conditional name="pnovo"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1672 <param name="pnovo_advanced" type="select" label="pNovo+ Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1673 <option value="yes">Advanced</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1674 <option value="no" selected="True">Default</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1675 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1676 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1677 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1678 <param name="pnovo_num_peptides" type="integer" value="10" label="pNovo+ number of peptides per spectrum, default is '10'."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1679 <param name="pnovo_lower_prec" type="integer" value="300" label="pNovo+ minimum precursor mass, default is '300'."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1680 <param name="pnovo_upper_prec" type="integer" value="5000" label="pNovo+ maximum precursor mass, default is '5000'."/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1681 <param name="pnovo_activation" type="select" label="pNovo+ activation type (HCD, CID or EDT)"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1682 <option value="HCD" selected="True">HCD</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1683 <option value="CID" >CID</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1684 <option value="EDT">EDT</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1685 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1686 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1687 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1688 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1689 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1690 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1691 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1692 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1693 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1694 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1695 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1696 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1697 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1698 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1699 <!-- ADVANCED PARAMETERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1700 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1701 <section name="advanced_options" expanded="false" title="Show/Hide advanced options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1702 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1703 <!-- SPECTRUM ANNOTATION --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1704 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1705 <section name="spectrum_annotation_options" expanded="false" title="Spectrum Annotation Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1706 <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1707 <validator type="in_range" min="0" max="1" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1708 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1709 <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="10" type="float" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1710 <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1711 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1712 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1713 <!-- SEQUENCE MATCHING --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1714 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1715 <section name="sequence_matching_options" expanded="false" title="Sequence Matching Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1716 <param name="sequence_matching_type" label="The peptide to protein sequence matching type" type="select"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1717 <option value="0">Character Sequence</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1718 <option value="1">Amino Acids</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1719 <option value="2" selected="true">Indistinguishable Amino Acids</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1720 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1721 <param name="sequence_matching_x" label="The maximal share of Xs in a sequence" help="0.25 means 25% of Xs" value="0.25" type="float"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1722 <validator type="in_range" min="0" max="1" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1723 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1724 <param name="sequence_matching_enzymatic_tags" label="Tags should only be mapped to enzymatic peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1725 <param name="sequence_matching_max_ptms_per_tag" label="The maximum number of PTMs per peptide when mapping tags" type="integer" value="3"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1726 <validator type="in_range" min="0" max="2147483647" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1727 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1728 <param name="sequence_matching_min_amino_acid_score" label="The minimum amino acid score when mapping tags" type="integer" value="30"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1729 <validator type="in_range" min="0" max="2147483647" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1730 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1731 <param name="sequence_matching_min_tag_length" label="The minimum tag length when mapping tags" type="integer" value="3"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1732 <validator type="in_range" min="0" max="2147483647" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1733 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1734 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1735 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1736 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1737 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1738 <!-- IMPORT FILTERS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1739 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1740 <section name="import_filters_options" expanded="false" title="Import filters"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1741 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="8" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1742 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1743 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" help="The higher precursor mass error allowed in order to filter out outliers" value="10" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1744 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select" > |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1745 <option value="1">ppm</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1746 <option value="0">Daltons</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1747 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1748 <param name="missed_cleavages_min" type="integer" label="Minimal number of missed cleavages to consider when importing identification files" help="Default is no filter" value="" optional="true"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1749 <param name="missed_cleavages_max" type="integer" label="Maximal number of missed cleavages to consider when importing identification files" help="Default is no filter" value="" optional="true"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1750 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" help="If true, peptides presenting unrecognized PTMs will be excluded" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1751 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1752 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1753 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1754 <!-- PTM LOCALIZATION --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1755 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1756 <section name="ptm_localization_options" expanded="false" title="PTM Localizacion"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1757 <conditional name="ptm_score"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1758 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1759 <option value="1" selected="True">PhosphoRS</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1760 <option value="2">None</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1761 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1762 <when value="1"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1763 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1764 <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="95.0" type="float" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1765 help="Automatic mode will be used if not set" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1766 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1767 <when value="2" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1768 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1769 <param name="ptm_sequence_matching_type" type="select" label="The modification to peptide sequence matching type." > |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1770 <option value="0">Character Sequence</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1771 <option value="1" selected="true">Amino Acids</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1772 <option value="2">Indistinguishable Amino Acids</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1773 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1774 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1775 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1776 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1777 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1778 <!-- GENE ANNOTATION --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1779 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1780 <section name="gene_annotation_options" expanded="false" title="Gene Annotation"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1781 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1782 label="gene mappings will be used and saved along with the project (UniProt databases only)" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1783 help="This should only be enabled for UniProt databaases" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1784 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1785 label="Update gene mappings automatically from Ensembl (UniProt databases only)" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1786 help="This should only be enabled for UniProt databaases" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1787 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1788 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1789 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1790 <!-- PROTEIN INFERENCE --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1791 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1792 <section name="protein_inference_options" expanded="false" title="Protein Inference"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1793 <conditional name="simplify_protein_groups_conditional"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1794 <param name="simplify_protein_groups_selector" type="select" label="Simplify protein groups"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1795 <option value="yes" selected="True">Yes</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1796 <option value="no">No</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1797 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1798 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1799 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1800 <param name="simplify_protein_groups_evidence" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1801 label="Based on Uniprot evidence level"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1802 <param name="simplify_protein_groups_confidence" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1803 label="Based on the peptide confidence"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1804 <param name="simplify_protein_groups_confidence_threshold" value="0.05" type="float" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1805 label="Confidence below which a peptide is ignored"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1806 <param name="simplify_protein_groups_enzymaticity" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1807 label="Based on Enzymaticity"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1808 <param name="simplify_protein_groups_variant" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1809 label="Based on Variant Mapping"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1810 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1811 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1812 <param name="simplify_protein_pi_modifications" type="boolean" truevalue="1" falsevalue="0" checked="true" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1813 label="Account for modifications when mapping peptides to proteins"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1814 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1815 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1816 <!-- VALIDATION LEVELS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1817 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1818 <section name="validation_levels_options" expanded="false" title="Validation Levels"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1819 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1820 <validator type="in_range" min="0" max="100" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1821 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1822 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1823 <validator type="in_range" min="0" max="100" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1824 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1825 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1826 <validator type="in_range" min="0" max="100" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1827 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1828 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1829 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1830 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1831 <!-- FRACTION ANALYSIS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1832 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1833 <section name="fraction_analysis_options" expanded="false" title="Fraction Analysis"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1834 <param name="protein_fraction_mw_confidence" value="95.0" type="float" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1835 label="Minimum confidence required for a protein in the fraction MW plot (in percentage)" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1836 help="default 95%: '95.0'"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1837 <validator type="in_range" min="0" max="100" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1838 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1839 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1840 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1841 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1842 <!-- DATABASE PROCESSING OPTIONS --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1843 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1844 <section name="database_processing_options" expanded="false" title="Database Processing Options"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1845 <conditional name="decoy_conditional"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1846 <param name="create_decoy_selector" type="select" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1847 label="Create a concatenated target/decoy database before running PeptideShaker" |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1848 help="Selecting this option will help PeptideShaker calculate FDR values"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1849 <option value="yes" selected="True">Yes</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1850 <option value="no" >No</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1851 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1852 <when value="no" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1853 <when value="yes"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1854 <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1855 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1856 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix"> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1857 <option value="0">Prefix</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1858 <option value="1" selected="True">Suffix</option> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1859 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1860 </when> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1861 </conditional> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1862 <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix."> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1863 </param> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1864 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1865 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1866 </section> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1867 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1868 </inputs> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1869 <outputs> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1870 <data name="Identification_Parameters_File" format="json" from_work_dir="IdentificationParametersOutput.par" label="${tool.name}: PAR file" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1871 </outputs> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1872 <tests> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1873 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1874 <!-- Test that default parameters generates a standard par file --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1875 <test> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1876 <param name="xtandem_advanced" value="yes"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1877 <param name="xtandem_refine_selector" value="no"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1878 <output name="Identification_Parameters_File" file="Identification_Parameters_default.par" ftype="json" compare="sim_size" delta="1000" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1879 </test> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1880 <!-- Test specific parameters with modifications --> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1881 <test> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1882 <param name="precursor_ion_tol" value="100"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1883 <param name="fixed_modifications" value="Carbamidomethylation of C"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1884 <param name="variable_modifications" value="Oxidation of M"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1885 <param name="min_charge" value="1"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1886 <param name="max_charge" value="3"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1887 <param name="xtandem_advanced" value="yes"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1888 <param name="xtandem_refine_selector" value="yes"/> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1889 <output name="Identification_Parameters_File" file="Identification_Parameters_specific.par" ftype="json" compare="sim_size" delta="1000" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1890 </test> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1891 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1892 </tests> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1893 <help> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1894 **What it does** |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1895 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1896 Creates a parameters file (.par) which can be used independently by SearchGUI or PeptideShaker apps. |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1897 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1898 A FASTA file with decoy sequences generated by FastaCLI is recommended if SearchGUI and PeptideShaker are going to use the output of this tool. |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1899 |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1900 </help> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1901 <expand macro="citations" /> |
bb0130ff73ce
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff
changeset
|
1902 </tool> |