fragpipe: msfragger_macros.xml annotate

annotate msfragger_macros.xml @ 7:b4f6df8fa89b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4

author	galaxyp
date	Wed, 01 Oct 2025 22:20:54 +0000
parents	59fec1e2a6c3
children

rev	line source
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1 <macros>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	2
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	3 <!-- Utility functions for linking input files -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	4 <token name="@CMD_IMPORTS@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	5 #import re
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	6 #def identifier_or_name($input1)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	7 #if hasattr($input1, 'element_identifier')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	8 #return $input1.element_identifier
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	9 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	10 #return $input1.name
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	11 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	12 #end def
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	13 #def clean($name1)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	14 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa\|fas\|fasta\|imzml\|mzml\|mzxml\|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	15 #return $name_clean
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	16 #end def
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	17 #def ln_name($ds)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	18 #set $ext = ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	19 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	20 #set $ext = ".mzML"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	21 #else if $ds.is_of_type('mzxml')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	22 #set $ext = ".mzXML"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	23 #else if $ds.is_of_type('mgf')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	24 #set $ext = ".mgf"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	25 #else if $ds.is_of_type('thermo.raw')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	26 #set $ext = ".raw"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	27 #else if $ds.is_of_type('fasta')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	28 #set $ext = ".fasta"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	29 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	30 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	31 #return $name
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	32 #end def
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	33 #set $i_names = []
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	34 #set $db_name = None
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	35 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	36
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	37 <!-- The following xml elements define the parameters for each given workflow -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	38 <xml name="msfragger_default">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	39 <expand macro="search_tolerances"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	40 <expand macro="digestion"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	41 <expand macro="variable_modification" mod_3="true"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	42 <expand macro="static_modification"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	43 <expand macro="glyco_labile"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	44 <expand macro="mass_offsets"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	45 <expand macro="spectrum_processing"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	46 <expand macro="open_search_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	47 <expand macro="modeling_output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	48 <expand macro="advanced_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	49 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	50 <xml name="msfragger_open">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	51 <expand macro="search_tolerances"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	52 <expand macro="digestion"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	53 <expand macro="variable_modification" mod_3="true"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	54 <expand macro="static_modification"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	55 <expand macro="glyco_labile"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	56 <expand macro="mass_offsets"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	57 <expand macro="spectrum_processing" mode_selected="false" mode_corrected="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	58 <expand macro="open_search_options" localize="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	59 <expand macro="modeling_output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	60 <expand macro="advanced_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	61 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	62 <xml name="msfragger_nonspecific_HLA">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	63 <expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/>
6 59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6 galaxyp parents: 5 diff changeset	64 <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false" digest_mass_range_min="200.0"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	65 <expand macro="variable_modification" mod_2="true" mod_group_hla="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	66 <expand macro="static_modification" check_cysteine="false"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	67 <expand macro="glyco_labile"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	68 <expand macro="mass_offsets"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	69 <expand macro="spectrum_processing" transform_none="false" transform_sqrt="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	70 <expand macro="open_search_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	71 <expand macro="modeling_output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	72 <expand macro="advanced_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	73 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	74 <xml name="msfragger_LFQ_MBR">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	75 <expand macro="search_tolerances"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	76 <expand macro="digestion"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	77 <expand macro="variable_modification" mod_3="true"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	78 <expand macro="static_modification"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	79 <expand macro="glyco_labile"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	80 <expand macro="mass_offsets"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	81 <expand macro="spectrum_processing"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	82 <expand macro="open_search_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	83 <expand macro="modeling_output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	84 <expand macro="advanced_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	85 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	86 <xml name="msfragger_TMT">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	87 <expand macro="search_tolerances"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	88 <expand macro="digestion" digest_mass_range_min="200.0"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	89 <expand macro="variable_modification" mod_3="true" mod_group_tmt="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	90 <expand macro="static_modification" lysine_value="229.16293"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	91 <expand macro="glyco_labile"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	92 <expand macro="mass_offsets"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	93 <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	94 <expand macro="open_search_options"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	95 <expand macro="modeling_output"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	96 <expand macro="advanced_options"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	97 </xml>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	98 <xml name="msfragger_dia_speclib_quant">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	99 <expand macro="search_tolerances"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	100 <expand macro="digestion" allowed_missed_cleavage_1="1" allowed_missed_cleavage_2="1"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	101 <expand macro="variable_modification" mod_1="true"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	102 <expand macro="static_modification"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	103 <expand macro="glyco_labile"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	104 <expand macro="mass_offsets"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	105 <expand macro="spectrum_processing" check_spectral_files="false"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	106 <expand macro="open_search_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	107 <expand macro="modeling_output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	108 <expand macro="advanced_options"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	109 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	110
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	111 <!--
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	112 The following elements define specific MSFragger configuration sections. Each xml macro is followed by a token element that enters
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	113 the parameters into a global msfragger_dict dictionary. This dictionary is used to generate a <configfile> configuration file.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	114 -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	115 <xml name="search_tolerances" token_precursor_ppm="false" token_precursor_da="false" token_precursor_mass_lower="-50" token_precursor_mass_upper="50" token_isotope_error="" token_fragment_mass_tolerance="20">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	116 <section name="search_tolerances" expanded="false" title="Search Tolerances">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	117
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	118 <conditional name="precursor">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	119 <param name="precursor_mass_units" type="select" label="Set Precursor Mass tolerances" help="Sets default parameters">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	120 <option value="default">Use default</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	121 <option value="ppm" selected="@PRECURSOR_PPM@">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	122 <option value="Da" selected="@PRECURSOR_DA@">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	123 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	124 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	125 <when value="ppm">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	126 <param argument="precursor_mass_lower" type="integer" value="@PRECURSOR_MASS_LOWER@" max="0" optional="true" label="Precursor mass tolerance lower bound" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	127 <param argument="precursor_mass_upper" type="integer" value="@PRECURSOR_MASS_UPPER@" min="0" optional="true" label="Precursor mass tolerance upper bound" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	128 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	129 <when value="Da">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	130 <param argument="precursor_mass_lower" type="float" max="0" optional="true" label="Precursor mass tolerance lower bound" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	131 <param argument="precursor_mass_upper" type="float" min="0" optional="true" label="Precursor mass tolerance upper bound" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	132 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	133 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	134
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	135 <conditional name="precursor_true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	136 <param name="precursor_true_units" type="select" label="Set Precursor True tolerance" help="STRONGLY recommended for open searches">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	137 <option value="default">Use default</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	138 <option value="ppm">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	139 <option value="Da">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	140 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	141 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	142 <when value="ppm">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	143 <param name="precursor_true_tolerance" type="integer" min="1" max="100" optional="true" label="Precursor true tolerance"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	144 help="True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches. Default: 0"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	145 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	146 <when value="Da">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	147 <param name="precursor_true_tolerance" type="float" min="0" max="10" optional="true" label="Precursor true tolerance"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	148 help="True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches. Default: 0"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	149 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	150 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	151
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	152 <conditional name="fragment">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	153 <param name="fragment_mass_units" type="select" label="Set Fragment Mass tolerances" help="Sets default parameters">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	154 <option value="default">Use default</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	155 <option value="ppm" selected="true">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	156 <option value="Da">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	157 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	158 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	159 <when value="ppm">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	160 <param name="fragment_mass_tolerance" type="integer" value="@FRAGMENT_MASS_TOLERANCE@" min="1" max="100" optional="true" label="Fragment mass tolerance"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	161 help="Fragment mass tolerance (window is +/- this value) Default: 20"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	162 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	163 <when value="Da">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	164 <param name="fragment_mass_tolerance" type="float" min="0" max="100" optional="true" label="Fragment mass tolerance"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	165 help="Fragment mass tolerance"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	166 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	167 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	168
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	169 <param argument="isotope_error" type="select" optional="true" label="Isotope error">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	170 <help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	171 Isotope correction for MS/MS events triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	172 </help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	173 <option value="0">0 - Disabled (for open search)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	174 <option value="0/1">0/1 - (Nonspecific)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	175 <option value="0/1/2">0/1/2 - (Correction for narrow window searches)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	176 <option value="0/1/2/3">0/1/2/3</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	177 <option value="-1/0/1/2/3">-1/0/1/2/3</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	178 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	179 <param argument="calibrate_mass" type="select" label="Calibration and Optimization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	180 <option value="0">0 - None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	181 <option value="1">1 - Mass calibration</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	182 <option value="2" selected="true">2 - Mass calibration, parameter optimization</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	183 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	184 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	185 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	186
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	187 <token name="@SEARCH_TOLERANCES@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	188 ## Search Tolerances
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	189
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	190 #if $prefix.search_tolerances.precursor.precursor_mass_units == 'Da'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	191 #set $msfragger_dict['precursor_mass_units'] = 0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	192 #elif $prefix.search_tolerances.precursor.precursor_mass_units == 'ppm'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	193 #set $msfragger_dict['precursor_mass_units'] = 1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	194 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	195 #if $prefix.search_tolerances.precursor.precursor_mass_units != 'default'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	196 #if $prefix.search_tolerances.precursor.precursor_mass_lower != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	197 #set $msfragger_dict['precursor_mass_lower'] = $prefix.search_tolerances.precursor.precursor_mass_lower
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	198 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	199 #if $prefix.search_tolerances.precursor.precursor_mass_upper != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	200 #set $msfragger_dict['precursor_mass_upper'] = $prefix.search_tolerances.precursor.precursor_mass_upper
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	201 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	202 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	203
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	204 #if $prefix.search_tolerances.precursor_true.precursor_true_units == 'Da'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	205 #set $msfragger_dict['precursor_true_units'] = 0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	206 #elif $prefix.search_tolerances.precursor_true.precursor_true_units == 'ppm'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	207 #set $msfragger_dict['precursor_true_units'] = 1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	208 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	209 #if $prefix.search_tolerances.precursor_true.precursor_true_units != 'default'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	210 #if $prefix.search_tolerances.precursor_true.precursor_true_tolerance != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	211 #set $msfragger_dict['precursor_true_tolerance'] = $prefix.search_tolerances.precursor_true.precursor_true_tolerance
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	212 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	213 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	214
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	215 #if $prefix.search_tolerances.fragment.fragment_mass_units == 'Da'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	216 #set $msfragger_dict['fragment_mass_units'] = 0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	217 #elif $prefix.search_tolerances.fragment.fragment_mass_units == 'ppm'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	218 #set $msfragger_dict['fragment_mass_units'] = 1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	219 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	220 #if $prefix.search_tolerances.fragment.fragment_mass_units != 'default'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	221 #if $prefix.search_tolerances.fragment.fragment_mass_tolerance != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	222 #set $msfragger_dict['fragment_mass_tolerance'] = $prefix.search_tolerances.fragment.fragment_mass_tolerance
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	223 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	224 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	225
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	226 #if $prefix.search_tolerances.isotope_error != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	227 #set $msfragger_dict['isotope_error'] = $prefix.search_tolerances.isotope_error
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	228 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	229 #if $prefix.search_tolerances.calibrate_mass != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	230 #set $msfragger_dict['calibrate_mass'] = $prefix.search_tolerances.calibrate_mass
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	231 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	232 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	233
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	234 <xml name="cleavage" token_search_enzyme_name="trypsin" token_cut="KR" token_nocut="P">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	235 <param name="search_enzyme_name" type="text" value="@SEARCH_ENZYME_NAME@"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	236 label="Digestion Enzyme" help="Name of enzyme to be written to the pepXML file."/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	237 <param name="search_enzyme_cut" type="text" value="@CUT@"
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	238 label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	239 <param name="search_enzyme_nocut" type="text" value="@NOCUT@"
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	240 label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore)"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	241 </xml>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	242 <xml name="digest" token_stricttrypsin="true" token_nonspecific="false" token_allowed_missed_cleavage="2">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	243 <conditional name="digest">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	244 <param name="search_enzyme" type="select" label="Protein Digestion Enzyme">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	245 <option value="trypsin">trypsin</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	246 <option value="stricttrypsin" selected="@STRICTTRYPSIN@">stricttrypsin</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	247 <option value="argc">argc</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	248 <option value="chymotrypsin">chymotrypsin</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	249 <option value="cnbr">cnbr</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	250 <option value="elastase">elastase</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	251 <option value="formicacid">formicacid</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	252 <option value="gluc">gluc</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	253 <option value="gluc_bicarb">gluc_bicarb</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	254 <option value="lysc">lysc</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	255 <option value="lysc-p">lysc-p</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	256 <option value="nonspecific" selected="@NONSPECIFIC@">nonspecific</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	257 <option value="custom">custom</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	258 <option value="trypsin/chymotrypsin">trypsin/chymotrypsin</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	259 <option value="trypsin/cnbr">trypsin/cnbr</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	260 <option value="trypsin_gluc">trypsin_gluc</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	261 <option value="trypsin_k">trypsin_k</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	262 <option value="trypsin_r">trypsin_r</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	263 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	264 <when value="trypsin">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	265 <expand macro="cleavage" search_enzyme_name="trypsin" cut="KR" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	266 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	267 <when value="stricttrypsin">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	268 <expand macro="cleavage" search_enzyme_name="stricttrypsin" cut="KR" nocut=""/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	269 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	270 <when value="argc">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	271 <expand macro="cleavage" search_enzyme_name="argc" cut="R" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	272 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	273 <when value="chymotrypsin">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	274 <expand macro="cleavage" search_enzyme_name="chymotrypsin" cut="FLWY" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	275 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	276 <when value="cnbr">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	277 <expand macro="cleavage" search_enzyme_name="cnbr" cut="M" nocut=""/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	278 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	279 <when value="elastase">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	280 <expand macro="cleavage" search_enzyme_name="elastase" cut="AGILV" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	281 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	282 <when value="formicacid">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	283 <expand macro="cleavage" search_enzyme_name="formicacid" cut="D" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	284 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	285 <when value="gluc">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	286 <expand macro="cleavage" search_enzyme_name="gluc" cut="DE" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	287 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	288 <when value="gluc_bicarb">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	289 <expand macro="cleavage" search_enzyme_name="gluc_bicarb" cut="E" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	290 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	291 <when value="lysc">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	292 <expand macro="cleavage" search_enzyme_name="lysc" cut="K" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	293 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	294 <when value="lysc-p">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	295 <expand macro="cleavage" search_enzyme_name="lysc-p" cut="K" nocut=""/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	296 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	297 <when value="nonspecific">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	298 <expand macro="cleavage" search_enzyme_name="nonspecific" cut="@" nocut=""/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	299 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	300 <when value="custom">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	301 <expand macro="cleavage" search_enzyme_name="custom" cut="" nocut=""/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	302 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	303 <when value="trypsin/chymotrypsin">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	304 <expand macro="cleavage" search_enzyme_name="trypsin/chymotrypsin" cut="FYWLKR" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	305 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	306 <when value="trypsin/cnbr">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	307 <expand macro="cleavage" search_enzyme_name="trypsin/cnbr" cut="KR" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	308 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	309 <when value="trypsin_gluc">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	310 <expand macro="cleavage" search_enzyme_name="trypsin_gluc" cut="DEKR" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	311 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	312 <when value="trypsin_k">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	313 <expand macro="cleavage" search_enzyme_name="trypsin_k" cut="K" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	314 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	315 <when value="trypsin_r">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	316 <expand macro="cleavage" search_enzyme_name="trypsin_r" cut="R" nocut="P"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	317 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	318 </conditional>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	319 <param name="allowed_missed_cleavage" type="integer" value="@ALLOWED_MISSED_CLEAVAGE@" min="0" max="5" optional="true"
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	320 label="Allowed number of missed cleavages"/>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	321 <param name="search_enzyme_sense" type="select" label="Search Enzyme Sense">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	322 <option value="C">C</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	323 <option value="N">N</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	324 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	325 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	326
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	327 <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0" token_allowed_missed_cleavage_1="2" token_allowed_missed_cleavage_2="2">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	328 <section name="digestion" expanded="false" title="In-silico Digestion Parameters">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	329 <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_1@"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	330 <conditional name="enzyme2">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	331 <param name="digest2" type="select" label="Second Enzyme Digest">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	332 <option value="no">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	333 <option value="yes">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	334 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	335 <when value="no"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	336 <when value="yes">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	337 <expand macro="digest" stricttrypsin="false" nonspecific="false" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_2@"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	338 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	339 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	340 <param name="num_enzyme_termini" type="select" label="Number of enzyme termini">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	341 <option value="0" selected="@TERMINI_0@">0 - non-enzymatic</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	342 <option value="1" selected="@TERMINI_1@">1 - semi-enzymatic</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	343 <option value="2" selected="@TERMINI_2@">2 - fully-enzymatic</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	344 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	345 <param name="digest_min_length" type="integer" value="7" min="1" max="30" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	346 label="Minimum length of peptides to be generated during in-silico digestion"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	347 <param name="digest_max_length" type="integer" value="@DIGEST_MAX_LENGTH@" min="10" max="100" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	348 label="Maximum length of peptides to be generated during in-silico digestion"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	349 <param name="digest_mass_range_min" type="float" value="@DIGEST_MASS_RANGE_MIN@" min="0.0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	350 label="Minimum Mass of peptides to be generated during in-silico digestion in Daltons" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	351 <param name="digest_mass_range_max" type="float" value="@DIGEST_MASS_RANGE_MAX@" min="0.0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	352 label="Maximum Mass of peptides to be generated during in-silico digestion in Daltons" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	353 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	354 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	355 <token name="@DIGESTION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	356 ## digest parameters
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	357 ##enzyme_1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	358 #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	359 #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	360 #if $prefix.digestion.search_enzyme_cut == '__at__'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	361 #set $msfragger_dict['search_enzyme_cut_1'] = '@'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	362 #else
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	363 #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	364 #end if
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	365 #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	366 #if $prefix.digestion.allowed_missed_cleavage != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	367 #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	368 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	369 #if $prefix.digestion.search_enzyme_sense != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	370 #set $msfragger_dict['search_enzyme_sense_1'] = $prefix.digestion.search_enzyme_sense
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	371 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	372 ##enzyme_2
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	373 #if $prefix.digestion.enzyme2.digest2 == 'yes'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	374 #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	375 #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	376 #if $prefix.digestion.enzyme2.digest.search_enzyme_cut == '__at__'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	377 #set $msfragger_dict['search_enzyme_cut_2'] = '@'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	378 #else
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	379 #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	380 #end if
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	381 #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	382 #if $prefix.digestion.enzyme2.allowed_missed_cleavage != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	383 #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	384 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	385 #if $prefix.digestion.enzyme2.search_enzyme_sense != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	386 #set $msfragger_dict['search_enzyme_sense_2'] = $prefix.digestion.enzyme2.search_enzyme_sense
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	387 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	388 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	389 #set $msfragger_dict['search_enzyme_sense_2'] = 'C'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	390 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	391 #if $prefix.digestion.num_enzyme_termini != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	392 #set $msfragger_dict['num_enzyme_termini'] = $prefix.digestion.num_enzyme_termini
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	393 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	394 #if $prefix.digestion.digest_min_length != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	395 #set $msfragger_dict['digest_min_length'] = $prefix.digestion.digest_min_length
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	396 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	397 #if $prefix.digestion.digest_max_length != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	398 #set $msfragger_dict['digest_max_length'] = $prefix.digestion.digest_max_length
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	399 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	400 #if $prefix.digestion.digest_mass_range_min != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	401 #set $msfragger_dict['misc.fragger.digest-mass-lo'] = $prefix.digestion.digest_mass_range_min
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	402 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	403 #if $prefix.digestion.digest_mass_range_min != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	404 #set $msfragger_dict['misc.fragger.digest-mass-hi'] = $prefix.digestion.digest_mass_range_max
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	405 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	406 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	407
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	408 <token name="@RE_FLOAT@">[+-]?\d+(\.\d*)?</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	409 <token name="@RE_AA@">([A-Z]+\|(c[A-Z])+\|(n[\^A-Z])+\|\[\^\|\])</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	410 <token name="@RE_MOD@">@RE_FLOAT@,@RE_AA@,\d</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	411 <token name="@RE_MODS@">@RE_MOD@(;\s@RE_MOD@)</token>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	412 <xml name="variable_modification" token_max_variable_mods_per_peptide="3" token_mod_1="false" token_mod_2="false" token_mod_3="false" token_mod_4="true" token_mod_group_hla="false" token_mod_group_tmt="false">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	413 <section name="variable_modification" expanded="false" title="Variable Modifications">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	414 <param name="max_variable_mods_per_peptide" type="integer" value="@MAX_VARIABLE_MODS_PER_PEPTIDE@" min="0" max="5" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	415 label="Maximum total number of variable modifications per peptide"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	416 <param name="variable_mods_select" type="select" optional="true" multiple="true" label="Select Variable Modifications">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	417 <option value="15.99491461956 M 1" selected="@MOD_1@">15.99491461956 M 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	418 <option value="15.99491461956 M 2" selected="@MOD_2@">15.99491461956 M 2</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	419 <option value="15.99491461956 M 3" selected="@MOD_3@">15.99491461956 M 3</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	420 <option value="42.0105646837 ntermsite^ 1" selected="@MOD_4@">42.0105646837 [^ 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	421 <option value="-17.0265 nQ 1" selected="@MOD_GROUP_HLA@">-17.0265 nQ 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	422 <option value="-18.0106 nE 1" selected="@MOD_GROUP_HLA@">-18.0106 nE 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	423 <option value="119.0041 C 1" selected="@MOD_GROUP_HLA@">119.0041 C 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	424 <option value="79.96633052074999 STY 3">79.96633052074999 STY 3</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	425 <option value="229.16293213472 n^ 1" selected="@MOD_GROUP_TMT@">229.16293213472 n^ 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	426 <option value="229.16293213472 S 1" selected="@MOD_GROUP_TMT@">229.16293213472 S 1</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	427 <option value="-18.0105646837 nE 1">-18.0105646837 nE 1</option>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	428 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	429 <param name="variable_mods" type="text" area="True" size="120x7" value="" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	430 label="Enter Variable Modifications">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	431 <help><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	432 Separate variable modifications with semicolons. Each modification has mass_change, residues, and max occurances values separated by commas.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	433 * is used to represent any amino acid
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	434 [ is a modifier for protein N-terminal
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	435 ] is a modifier for protein C-terminal
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	436 n is a modifier for peptide N-terminal
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	437 c is a modifier for peptide C-terminal
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	438 Syntax Examples:
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	439 15.9949,M,3 (for oxidation on methionine)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	440 79.66331,STY,1 (for phosphorylation)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	441 -17.0265,nQnC,1 (for pyro-Glu or loss of ammonia at peptide N-terminal)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	442 Example (M oxidation and N-terminal acetylation):
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	443 15.9949,M,3;42.0106,[*,1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	444 ]]></help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	445 <validator type="regex">^\s@RE_MODS@\s$</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	446 <sanitizer sanitize="False"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	447 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	448
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	449 <param name="use_all_mods_in_first_search" type="select" optional="true" label="Use all variable modifications in first search">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	450 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	451 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	452 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	453 <param name="clip_nTerm_M" type="select" optional="true" label="Trim protein N-terminal methionine as a variable modification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	454 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	455 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	456 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	457
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	458 <param name="max_variable_mods_combinations" type="integer" value="5000" min="0" max="65534" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	459 label="Maximum allowed number of modified variably modified peptides from each peptide sequence"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	460 help="If a greater number than the maximum is generated, only the unmodified peptide is considered."/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	461 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	462 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	463 <token name="@VARIABLE_MODIFICATION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	464 ## Variable Modification Parameters
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	465 #if $prefix.variable_modification.max_variable_mods_per_peptide != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	466 #set $msfragger_dict['max_variable_mods_per_peptide'] = $prefix.variable_modification.max_variable_mods_per_peptide
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	467 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	468 ##maximum of 7 mods - amino acid codes, * for any amino acid, [ and ] specifies protein termini, n and c specifies peptide termini
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	469 ##variable_mod_01=15.9949 M
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	470 ##variable_mod_02=42.0106 [*
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	471 ##variable_mod_03=79.96633 STY
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	472 ##variable_mod_03=-17.0265 nQnC
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	473 ##variable_mod_04=-18.0106 nE
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	474 ##
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	475 #if $prefix.variable_modification.use_all_mods_in_first_search != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	476 #set $msfragger_dict['use_all_mods_in_first_search'] = $prefix.variable_modification.use_all_mods_in_first_search
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	477 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	478 #if $prefix.variable_modification.clip_nTerm_M != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	479 #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	480 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	481 #if $prefix.variable_modification.max_variable_mods_combinations != "None"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	482 #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	483 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	484 #set $vmods = []
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	485 #if $prefix.variable_modification.variable_mods_select != 'None'
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	486 #set $vmods = [x.replace(' ',',').replace('ntermsite','[') for x in str($prefix.variable_modification.variable_mods_select).split(',')]
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	487 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	488 #if $prefix.variable_modification.variable_mods != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	489 #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')]
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	490 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	491 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	492
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	493 <xml name="static_modification" token_check_cysteine="true" token_lysine_value="0.0">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	494 <section name="static_modification" expanded="false" title="Static Modifications">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	495 <param name="add_Cterm_peptide_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	496 label="Statically add mass in Da to C-terminal of peptide"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	497 <param name="add_Cterm_peptide" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	498 label="Statically add mass in Da to C-terminal of peptide" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	499
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	500 <param name="add_Nterm_peptide_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	501 label="Statically add mass in Da to N-terminal of peptide"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	502 <param name="add_Nterm_peptide" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	503 label="Statically add mass in Da to N-terminal of peptide" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	504
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	505 <param name="add_Cterm_protein_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	506 label="Statically add mass in Da to C-terminal of protein"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	507 <param name="add_Cterm_protein" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	508 label="Statically add mass in Da to C-terminal of protein" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	509
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	510 <param name="add_Nterm_protein_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	511 label="Statically add mass in Da to N-terminal of protein"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	512 <param name="add_Nterm_protein" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	513 label="Statically add mass in Da to N-terminal of protein" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	514
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	515 <param name="add_A_alanine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	516 label="Statically add mass in Da to A (alanine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	517 <param name="add_A_alanine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	518 label="Statically add mass in Da to A (alanine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	519
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	520 <param name="add_R_arginine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	521 label="Statically add mass in Da to R (arginine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	522 <param name="add_R_arginine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	523 label="Statically add mass in Da to R (arginine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	524
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	525 <param name="add_N_asparagine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	526 label="Statically add mass in Da to N (asparagine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	527 <param name="add_N_asparagine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	528 label="Statically add mass in Da to N (asparagine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	529
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	530 <param name="add_D_aspartic_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	531 label="Statically add mass in Da to D (aspartic_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	532 <param name="add_D_aspartic_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	533 label="Statically add mass in Da to D (aspartic_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	534
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	535 <param name="add_C_cysteine_bool" type="boolean" checked="@CHECK_CYSTEINE@"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	536 label="Statically add mass in Da to C (cysteine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	537 <param name="add_C_cysteine" type="float" value="57.02146"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	538 label="Statically add mass in Da to C (cysteine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	539
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	540 <param name="add_E_glutamic_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	541 label="Statically add mass in Da to E (glutamic_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	542 <param name="add_E_glutamic_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	543 label="Statically add mass in Da to E (glutamic_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	544
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	545 <param name="add_Q_glutamine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	546 label="Statically add mass in Da to Q (glutamine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	547 <param name="add_Q_glutamine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	548 label="Statically add mass in Da to Q (glutamine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	549
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	550 <param name="add_G_glycine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	551 label="Statically add mass in Da to G (glycine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	552 <param name="add_G_glycine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	553 label="Statically add mass in Da to G (glycine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	554
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	555 <param name="add_H_histidine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	556 label="Statically add mass in Da to H (histidine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	557 <param name="add_H_histidine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	558 label="Statically add mass in Da to H (histidine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	559
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	560 <param name="add_I_isoleucine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	561 label="Statically add mass in Da to I (isoleucine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	562 <param name="add_I_isoleucine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	563 label="Statically add mass in Da to I (isoleucine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	564
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	565 <param name="add_L_leucine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	566 label="Statically add mass in Da to L (leucine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	567 <param name="add_L_leucine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	568 label="Statically add mass in Da to L (leucine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	569
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	570 <param name="add_K_lysine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	571 label="Statically add mass in Da to K (lysine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	572 <param name="add_K_lysine" type="float" value="@LYSINE_VALUE@"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	573 label="Statically add mass in Da to K (lysine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	574
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	575 <param name="add_M_methionine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	576 label="Statically add mass in Da to M (methionine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	577 <param name="add_M_methionine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	578 label="Statically add mass in Da to M (methionine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	579
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	580 <param name="add_F_phenylalanine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	581 label="Statically add mass in Da to F (phenylalanine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	582 <param name="add_F_phenylalanine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	583 label="Statically add mass in Da to F (phenylalanine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	584
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	585 <param name="add_P_proline_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	586 label="Statically add mass in Da to P (proline)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	587 <param name="add_P_proline" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	588 label="Statically add mass in Da to P (proline)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	589
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	590 <param name="add_S_serine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	591 label="Statically add mass in Da to S (serine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	592 <param name="add_S_serine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	593 label="Statically add mass in Da to S (serine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	594
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	595 <param name="add_T_threonine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	596 label="Statically add mass in Da to T (threonine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	597 <param name="add_T_threonine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	598 label="Statically add mass in Da to T (threonine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	599
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	600 <param name="add_W_tryptophan_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	601 label="Statically add mass in Da to W (tryptophan)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	602 <param name="add_W_tryptophan" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	603 label="Statically add mass in Da to W (tryptophan)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	604
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	605 <param name="add_Y_tyrosine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	606 label="Statically add mass in Da to Y (tyrosine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	607 <param name="add_Y_tyrosine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	608 label="Statically add mass in Da to Y (tyrosine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	609
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	610 <param name="add_V_valine_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	611 label="Statically add mass in Da to V (valine)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	612 <param name="add_V_valine" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	613 label="Statically add mass in Da to V (valine)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	614
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	615 <param name="add_B_user_amino_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	616 label="Statically add mass in Da to B (iuser_amino_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	617 <param name="add_B_user_amino_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	618 label="Statically add mass in Da to B (iuser_amino_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	619
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	620 <param name="add_J_user_amino_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	621 label="Statically add mass in Da to J (iuser_amino_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	622 <param name="add_J_user_amino_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	623 label="Statically add mass in Da to J (iuser_amino_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	624
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	625 <param name="add_O_user_amino_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	626 label="Statically add mass in Da to O (user_amino_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	627 <param name="add_O_user_amino_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	628 label="Statically add mass in Da to O (user_amino_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	629
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	630 <param name="add_U_user_amino_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	631 label="Statically add mass in Da to U (iuser_amino_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	632 <param name="add_U_user_amino_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	633 label="Statically add mass in Da to U (iuser_amino_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	634
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	635 <param name="add_X_user_amino_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	636 label="Statically add mass in Da to X (iuser_amino_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	637 <param name="add_X_user_amino_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	638 label="Statically add mass in Da to X (iuser_amino_acid)" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	639
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	640 <param name="add_Z_user_amino_acid_bool" type="boolean" checked="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	641 label="Statically add mass in Da to Z (iuser_amino_acid)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	642 <param name="add_Z_user_amino_acid" type="float" value="0.0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	643 label="Statically add mass in Da to Z (iuser_amino_acid)" />
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	644 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	645 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	646 <token name="@STATIC_MODIFICATION@"><![CDATA[
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	647 #set $fmod_vals = {}
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	648 #set $fmod_vals['add_Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	649 #set $fmod_vals['add_Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	650 #set $fmod_vals['add_Cterm_protein'] = $prefix.static_modification.add_Cterm_protein
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	651 #set $fmod_vals['add_Nterm_protein'] = $prefix.static_modification.add_Nterm_protein
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	652 #set $fmod_vals['add_G_glycine'] = $prefix.static_modification.add_G_glycine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	653 #set $fmod_vals['add_A_alanine'] = $prefix.static_modification.add_A_alanine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	654 #set $fmod_vals['add_S_serine'] = $prefix.static_modification.add_S_serine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	655 #set $fmod_vals['add_P_proline'] = $prefix.static_modification.add_P_proline
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	656 #set $fmod_vals['add_V_valine'] = $prefix.static_modification.add_V_valine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	657 #set $fmod_vals['add_T_threonine'] = $prefix.static_modification.add_T_threonine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	658 #set $fmod_vals['add_C_cysteine'] = $prefix.static_modification.add_C_cysteine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	659 #set $fmod_vals['add_L_leucine'] = $prefix.static_modification.add_L_leucine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	660 #set $fmod_vals['add_I_isoleucine'] = $prefix.static_modification.add_I_isoleucine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	661 #set $fmod_vals['add_N_asparagine'] = $prefix.static_modification.add_N_asparagine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	662 #set $fmod_vals['add_D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	663 #set $fmod_vals['add_Q_glutamine'] = $prefix.static_modification.add_Q_glutamine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	664 #set $fmod_vals['add_K_lysine'] = $prefix.static_modification.add_K_lysine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	665 #set $fmod_vals['add_E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	666 #set $fmod_vals['add_M_methionine'] = $prefix.static_modification.add_M_methionine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	667 #set $fmod_vals['add_H_histidine'] = $prefix.static_modification.add_H_histidine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	668 #set $fmod_vals['add_F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	669 #set $fmod_vals['add_R_arginine'] = $prefix.static_modification.add_R_arginine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	670 #set $fmod_vals['add_Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	671 #set $fmod_vals['add_W_tryptophan'] = $prefix.static_modification.add_W_tryptophan
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	672 #set $fmod_vals['add_B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	673 #set $fmod_vals['add_J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	674 #set $fmod_vals['add_O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	675 #set $fmod_vals['add_U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	676 #set $fmod_vals['add_X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	677 #set $fmod_vals['add_Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	678
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	679 #set $fmod_bools = {}
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	680 #set $fmod_bools['add_Cterm_peptide_bool'] = $prefix.static_modification.add_Cterm_peptide_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	681 #set $fmod_bools['add_Nterm_peptide_bool'] = $prefix.static_modification.add_Nterm_peptide_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	682 #set $fmod_bools['add_Cterm_protein_bool'] = $prefix.static_modification.add_Cterm_protein_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	683 #set $fmod_bools['add_Nterm_protein_bool'] = $prefix.static_modification.add_Nterm_protein_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	684 #set $fmod_bools['add_G_glycine_bool'] = $prefix.static_modification.add_G_glycine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	685 #set $fmod_bools['add_A_alanine_bool'] = $prefix.static_modification.add_A_alanine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	686 #set $fmod_bools['add_S_serine_bool'] = $prefix.static_modification.add_S_serine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	687 #set $fmod_bools['add_P_proline_bool'] = $prefix.static_modification.add_P_proline_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	688 #set $fmod_bools['add_V_valine_bool'] = $prefix.static_modification.add_V_valine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	689 #set $fmod_bools['add_T_threonine_bool'] = $prefix.static_modification.add_T_threonine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	690 #set $fmod_bools['add_C_cysteine_bool'] = $prefix.static_modification.add_C_cysteine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	691 #set $fmod_bools['add_L_leucine_bool'] = $prefix.static_modification.add_L_leucine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	692 #set $fmod_bools['add_I_isoleucine_bool'] = $prefix.static_modification.add_I_isoleucine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	693 #set $fmod_bools['add_N_asparagine_bool'] = $prefix.static_modification.add_N_asparagine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	694 #set $fmod_bools['add_D_aspartic_acid_bool'] = $prefix.static_modification.add_D_aspartic_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	695 #set $fmod_bools['add_Q_glutamine_bool'] = $prefix.static_modification.add_Q_glutamine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	696 #set $fmod_bools['add_K_lysine_bool'] = $prefix.static_modification.add_K_lysine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	697 #set $fmod_bools['add_E_glutamic_acid_bool'] = $prefix.static_modification.add_E_glutamic_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	698 #set $fmod_bools['add_M_methionine_bool'] = $prefix.static_modification.add_M_methionine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	699 #set $fmod_bools['add_H_histidine_bool'] = $prefix.static_modification.add_H_histidine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	700 #set $fmod_bools['add_F_phenylalanine_bool'] = $prefix.static_modification.add_F_phenylalanine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	701 #set $fmod_bools['add_R_arginine_bool'] = $prefix.static_modification.add_R_arginine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	702 #set $fmod_bools['add_Y_tyrosine_bool'] = $prefix.static_modification.add_Y_tyrosine_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	703 #set $fmod_bools['add_W_tryptophan_bool'] = $prefix.static_modification.add_W_tryptophan_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	704 #set $fmod_bools['add_B_user_amino_acid_bool'] = $prefix.static_modification.add_B_user_amino_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	705 #set $fmod_bools['add_J_user_amino_acid_bool'] = $prefix.static_modification.add_J_user_amino_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	706 #set $fmod_bools['add_O_user_amino_acid_bool'] = $prefix.static_modification.add_O_user_amino_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	707 #set $fmod_bools['add_U_user_amino_acid_bool'] = $prefix.static_modification.add_U_user_amino_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	708 #set $fmod_bools['add_X_user_amino_acid_bool'] = $prefix.static_modification.add_X_user_amino_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	709 #set $fmod_bools['add_Z_user_amino_acid_bool'] = $prefix.static_modification.add_Z_user_amino_acid_bool
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	710
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	711 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	712
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	713 <xml name="spectrum_processing" token_mode_selected="true" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false" token_check_spectral_files="true">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	714 <section name="spectrum_processing" expanded="false" title="Spectrum Processing">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	715 <param name="precursor_mass_mode" type="select" label="Precursor mass mode">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	716 <option value="isolated" selected="@MODE_ISOLATED@">isolated</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	717 <option value="selected" selected="@MODE_SELECTED@">selected</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	718 <option value="corrected" selected="@MODE_CORRECTED@">corrected</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	719 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	720 <param name="minimum_peaks" type="integer" value="" min="0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	721 label="Minimum number of peaks in experimental spectrum for matching" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	722 <param name="use_topN_peaks" type="integer" value="" min="0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	723 label="Pre-process experimental spectrum to only use top N peaks" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	724 <param name="minimum_ratio" type="float" value="" min="0.0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	725 label="Filter peaks by minimum_ratio of base peak"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	726 help="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensit Default: 0.0" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	727 <conditional name="precursor">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	728 <param name="override_charge" type="select" label="Precursor Charge Override" help="override_charge">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	729 <option value="default">Use default</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	730 <option value="false">Use precursor charge</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	731 <option value="true" selected="@OVERRIDE_CHARGE@">Ignore precursor charge and set range</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	732 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	733 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	734 <when value="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	735 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	736 <param name="precursor_charge_min" type="integer" value="1" min="0" max="6"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	737 label="Minimum Potential Precursor Charge" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	738 <param name="precursor_charge_max" type="integer" value="4" min="0" max="8"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	739 label="Maximum Potential Precursor Charge" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	740 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	741 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	742 <section name="clear" expanded="false" title="Clear mz range for iTRAQ/TMT experiments">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	743 <param name="clear_mz_range_min" type="float" value="@CLEAR_MZ_RANGE_MIN@" min="0.0" optional="true" label="Minimum of m/z range to remove" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	744 <param name="clear_mz_range_max" type="float" value="@CLEAR_MZ_RANGE_MAX@" min="0.0" optional="true" label="Maximum of m/z range to remove" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	745 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	746 <param name="remove_precursor_peak" type="select" optional="true" label="Remove precursor peak">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	747 <option value="0" selected="@RM_PEAK0@">do not remove</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	748 <option value="1" selected="@RM_PEAK1@">remove the peak with precursor charge</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	749 <option value="2" selected="@RM_PEAK2@">remove the peaks with all charge states (only for DDA mode)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	750 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	751 <param name="remove_precursor_range_min" type="float" value="-1.5" min="-10.0" max="0.0" optional="true" label="Minimum of precursor m/z range to remove" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	752 <param name="remove_precursor_range_max" type="float" value="1.5" min="0.0" max="10.0" optional="true" label="Maximum of precursor m/z range to remove" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	753 <param name="intensity_transform" type="select" label="Intensity transform">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	754 <option value="0" selected="@TRANSFORM_NONE@">None, not removed</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	755 <option value="1" selected="@TRANSFORM_SQRT@">Square root</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	756 </param>
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	757 <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="@CHECK_SPECTRAL_FILES@" label="Check spectral files"/>
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	758 <param name="require_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require precursor"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	759 <param name="reuse_dia_fragment_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Reuse DIA fragment peaks"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	760 <param name="activation_types" type="select" optional="true" label="Activation Type Filter">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	761 <option value="all" selected="true">all</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	762 <option value="HCD">HCD</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	763 <option value="ETD">ETD</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	764 <option value="CID">CID</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	765 <option value="ECD">ECD</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	766 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	767 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	768 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	769 <token name="@SPECTRUM_PROCESSING@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	770 ## spectral processing
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	771 #if $prefix.spectrum_processing.precursor_mass_mode != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	772 #set $msfragger_dict['precursor_mass_mode'] = $prefix.spectrum_processing.precursor_mass_mode
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	773 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	774 #if $prefix.spectrum_processing.minimum_peaks != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	775 #set $msfragger_dict['minimum_peaks'] = $prefix.spectrum_processing.minimum_peaks
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	776 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	777 #if $prefix.spectrum_processing.use_topN_peaks != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	778 #set $msfragger_dict['use_topN_peaks'] = $prefix.spectrum_processing.use_topN_peaks
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	779 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	780 #if $prefix.spectrum_processing.minimum_ratio != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	781 #set $msfragger_dict['minimum_ratio'] = $prefix.spectrum_processing.minimum_ratio
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	782 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	783 #if $prefix.spectrum_processing.precursor.override_charge != 'default'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	784 #set $msfragger_dict['override_charge'] = $prefix.spectrum_processing.precursor.override_charge
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	785 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	786 #if $prefix.spectrum_processing.precursor.override_charge == 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	787 #if $prefix.spectrum_processing.precursor.precursor_charge_min != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	788 #set $msfragger_dict['misc.fragger.precursor-charge-lo'] = $prefix.spectrum_processing.precursor.precursor_charge_min
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	789 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	790 #if $prefix.spectrum_processing.precursor.precursor_charge_max != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	791 #set $msfragger_dict['misc.fragger.precursor-charge-hi'] = $prefix.spectrum_processing.precursor.precursor_charge_max
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	792 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	793 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	794 #if $prefix.spectrum_processing.clear.clear_mz_range_min != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	795 #set $msfragger_dict['misc.fragger.clear-mz-lo'] = $prefix.spectrum_processing.clear.clear_mz_range_min
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	796 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	797 #if $prefix.spectrum_processing.clear.clear_mz_range_max != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	798 #set $msfragger_dict['misc.fragger.clear-mz-hi'] = $prefix.spectrum_processing.clear.clear_mz_range_max
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	799 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	800 #if $prefix.spectrum_processing.remove_precursor_peak != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	801 #set $msfragger_dict['remove_precursor_peak'] = $prefix.spectrum_processing.remove_precursor_peak
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	802 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	803 #if $prefix.spectrum_processing.remove_precursor_range_min != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	804 #set $msfragger_dict['misc.fragger.remove-precursor-range-lo'] = $prefix.spectrum_processing.remove_precursor_range_min
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	805 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	806 #if $prefix.spectrum_processing.remove_precursor_range_max != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	807 #set $msfragger_dict['misc.fragger.remove-precursor-range-hi'] = $prefix.spectrum_processing.remove_precursor_range_max
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	808 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	809
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	810 #if $prefix.spectrum_processing.intensity_transform != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	811 #set $msfragger_dict['intensity_transform'] = $prefix.spectrum_processing.intensity_transform
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	812 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	813
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	814 #set $msfragger_dict['check_spectral_files'] = $prefix.spectrum_processing.check_spectral_files
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	815 #set $msfragger_dict['require_precursor'] = $prefix.spectrum_processing.require_precursor
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	816 #set $msfragger_dict['reuse_dia_fragment_peaks'] = $prefix.spectrum_processing.reuse_dia_fragment_peaks
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	817
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	818 #if $prefix.spectrum_processing.activation_types != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	819 #set $msfragger_dict['activation_types'] = $prefix.spectrum_processing.activation_types
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	820 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	821 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	822
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	823 <xml name="open_search_options" token_localize="false" token_mass_diff_to_variable_mod0="true" token_mass_diff_to_variable_mod1="false" token_mass_diff_to_variable_mod2="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	824 <section name="open_search" expanded="false" title="Open Search Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	825 <param name="mass_diff_to_variable_mod" type="select" label="Report mass shift as a variable mod">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	826 <option value="0" selected="@MASS_DIFF_TO_VARIABLE_MOD0@">0 - No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	827 <option value="1" selected="@MASS_DIFF_TO_VARIABLE_MOD1@">1 - yes and remove delta mass</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	828 <option value="2" selected="@MASS_DIFF_TO_VARIABLE_MOD2@">2 - yes and keep delta mass</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	829 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	830 <param name="track_zero_topN" type="integer" value="" min="0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	831 label="Track top N unmodified peptide results" >
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	832 <help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	833 Track top N unmodified peptide results separately from main results internally for boosting features.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	834 Should be set to a number greater than output_report_topN if zero bin boosting is desired.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	835 Default: 0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	836 </help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	837 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	838 <param name="zero_bin_accept_expect" type="float" value="" min="0.0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	839 label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value."
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	840 help="Default: 0.0" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	841 <param name="zero_bin_mult_expect" type="float" value="" min="0.0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	842 label="Multiplies expect value of PSMs in the zero-bin during results ordering"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	843 help="(set to less than 1 for boosting) Default: 1.0" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	844 <param name="delta_mass_exclude_ranges_min" type="float" value="-1.5" label="Delta mass exclude range minimum" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	845 <param name="delta_mass_exclude_ranges_max" type="float" value="3.5" label="Delta mass exclude range maximum" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	846 <param name="localize_delta_mass" type="boolean" truevalue="true" falsevalue="false" checked="@LOCALIZE@"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	847 label="Localize mass shift (LOS)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	848 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	849 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	850 <token name="@OPEN_SEARCH@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	851 ##open search parameters
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	852 #if $prefix.open_search.mass_diff_to_variable_mod != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	853 #set $msfragger_dict['mass_diff_to_variable_mod'] = $prefix.open_search.mass_diff_to_variable_mod
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	854 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	855 #if $prefix.open_search.track_zero_topN != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	856 #set $msfragger_dict['track_zero_topN'] = $prefix.open_search.track_zero_topN
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	857 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	858 #if $prefix.open_search.zero_bin_accept_expect != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	859 #set $msfragger_dict['zero_bin_accept_expect'] = $prefix.open_search.zero_bin_accept_expect
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	860 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	861 #if $prefix.open_search.zero_bin_mult_expect != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	862 #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	863 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	864 #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	865 #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	866 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	867
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	868 <xml name="modeling_output">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	869 <section name="modeling_output" expanded="false" title="Modeling and Output">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	870 <param name="min_fragments_modelling" type="integer" min="1" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	871 label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	872 <param name="min_matched_fragments" type="integer" min="1" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	873 label="Minimum number of matched peaks for PSM to be reported"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	874 help="recommend a minimum of 4 for narrow window searching and 6 for open searches"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	875 <param name="max_fragment_charge" type="integer" min="1" max="4" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	876 label="Maximum fragment_charge Default:2"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	877 help="recommend a minimum of 4 for narrow window searching and 6 for open searches"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	878 <param name="deisotope" type="select" label="Deisotope" optional="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	879 <option value="0">0 - No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	880 <option value="1">1 - yes and assume singleton peaks single charged</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	881 <option value="2">2 - yes and assume singleton peaks single or double charged</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	882 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	883 <param name="deneutralloss" type="boolean" truevalue="1" falsevalue="0" checked="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	884 label="Perform deneutrallossing"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	885 <param name="fragment_ion_series" type="select" value="b,y" label="Fragment ion_series" optional="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	886 <option value="b,y">b,y</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	887 <option value="b,y,Y">b,y,Y</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	888 <option value="b,y,c,z">b,y,c,z</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	889 <option value="b,y,c,z,Y">b,y,c,z,Y</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	890 <option value="b,y,b~,y~,Y">b,y,b~,y~,Y</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	891 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	892 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	893 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	894 <token name="@MODELING_OUTPUT@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	895 ##Peak matching
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	896 #if $prefix.modeling_output.min_fragments_modelling != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	897 #set $msfragger_dict['min_fragments_modelling'] = $prefix.modeling_output.min_fragments_modelling
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	898 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	899 #if $prefix.modeling_output.min_matched_fragments != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	900 #set $msfragger_dict['min_matched_fragments'] = $prefix.modeling_output.min_matched_fragments
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	901 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	902 #if $prefix.modeling_output.max_fragment_charge != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	903 #set $msfragger_dict['max_fragment_charge'] = $prefix.modeling_output.max_fragment_charge
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	904 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	905 #if $prefix.modeling_output.deisotope != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	906 #set $msfragger_dict['deisotope'] = $prefix.modeling_output.deisotope
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	907 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	908 #set $msfragger_dict['deneutralloss'] = $prefix.modeling_output.deneutralloss
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	909 #if $prefix.modeling_output.fragment_ion_series != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	910 #set $msfragger_dict['fragment_ion_series'] = $prefix.modeling_output.fragment_ion_series
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	911 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	912 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	913
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	914 <!-- Tokens used in the mass_offsets section. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	915 <token name="@MASS_OFFSET_LABILE_ADP-RIBOSYLATION@">0/541.06111</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	916 <token name="@MASS_OFFSET_LABILE_PHOSPHO@">0/79.966331</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	917 <token name="@MASS_OFFSET_MASS-OFFSET-COMMONPTMS@">-105.0248 -89.0299 -33.9877 -32.0085 -30.0106 -18.0106 -17.0265 -2.0157 -1.007825 -0.984 0 0.984 3.9949 12.0 13.9793 14.0157 15.9949 19.9898 21.969392 21.9819 23.95806 26.0157 27.9949 28.0313 28.990164 29.9742 31.972071 31.9898 37.9469 37.955882 42.0106 42.047 43.0058 43.9898 44.985078 47.9847 53.9193 57.02146 58.0055 61.9135 61.921774 68.026215 70.041865 71.0371 79.9568 79.9663 86.000394 100.016 114.042927 119.004099 128.095 146.0579 156.1011 162.0528 173.051 176.0321 178.0477 183.035399 189.046 203.0794 204.1878 210.1984 228.111 229.014009 238.2297 301.9865 340.1006 349.1373 365.1322 365.1322 406.1587 541.06111</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	918 <token name="@XRNAX-MASSOFFSET@">0 306.025302 324.035867 612.051 611.067 630.061 629.077 635.078 651.073 653.088 669.083 151.994 918.076 917.092 936.086 916.108 935.102 934.118 941.103 957.098 940.119 956.114 959.114 975.109 958.13 974.125 964.13 980.125 996.12 982.141 998.136 1014.13</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	919 <token name="@FPOP@">0 15.9949 31.989829 47.984744 13.979265 -43.053433 -22.031969 -23.015984 -10.031969 4.9735 -30.010565 -27.994915 -43.989829 -25.031631 -9.036716</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	920 <token name="@MASS_OFFSET_GLYCO-N@">0 568.21156 892.3172 1038.375109 1054.37002 1095.39657 1200.427929 1216.42284 1241.454479 1257.44939 1298.47594 1362.480749 1378.47566 1387.512388 1403.507299 1419.50221 1444.533849 1460.52876 1501.55531 1524.533569 1533.570297 1540.52848 1548.5448065 1549.565208 1565.560119 1581.55503 1589.5713565 1606.586669 1622.58158 1647.613219 1663.60813 1686.586389 1694.6027155 1695.623117 1702.5813 1704.63468 1710.5976265 1711.618028 1727.612939 1735.6292655 1736.649667 1751.6241765 1752.644578 1768.639489 1784.6344 1793.671128 1809.666039 1825.66095 1848.639209 1850.692589 1856.6555355 1857.675937 1864.63412 1866.6875 1872.6504465 1873.670848 1880.666773 1889.665759 1897.6820855 1898.702487 1907.71405 1913.6769965 1914.697398 1930.692309 1938.7086355 1946.68722 1954.7035465 1955.723948 1971.718859 1987.71377 1996.750498 2010.692029 2012.745409 2018.7083555 2019.728757 2026.68694 2028.74032 2042.719593 2043.7399945 2053.771959 2059.7349055 2060.755307 2069.76687 2075.7298165 2076.750218 2092.745129 2100.7614555 2101.781857 2108.74004 2110.79342 2116.7563665 2117.776768 2133.771679 2141.7880055 2142.808407 2157.7829165 2158.803318 2172.744849 2174.798229 2188.73976 2190.79314 2204.772413 2205.7928145 2206.813216 2215.824779 2221.7877255 2222.808127 2231.81969 2237.7826365 2245.798963 2246.8193645 2254.797949 2256.851329 2262.8142755 2263.834677 2270.79286 2278.8091865 2279.829588 2287.8459145 2313.87279 2320.856138 2334.797669 2336.851049 2350.79258 2350.830322 2352.84596 2352.871125 2366.825233 2391.856872 2393.87251 2407.851783 2408.8721845 2424.8670955 2425.887497 2432.883422 2434.89906 2448.878333 2457.877319 2459.930699 2463.8402655 2465.8936455 2475.92561 2481.8885565 2498.903869 2528.878053 2539.930419 2545.8933655 2553.909692 2555.92533 2569.904603 2570.9250045 2571.945406 2580.956969 2586.9199155 2621.983519 2627.9464655 2643.9413765 2644.961778 2674.935962 2701.983239 2715.962512 2716.9829135 2717.97815 2772.983973 2775.024776 2786.963246 2789.9992855 2791.019687 2798.015612000001 2814.010523 2823.009509 2861.0000195 2864.036059 2871.057149 2878.015332 2880.03097 2896.051046 2919.041882 2935.036793 2937.077596 2966.0313785 2968.0470165 3007.0579285 3009.0735665 3010.119133 3048.0844785 3064.0793895 3081.094702 3083.11034 3083.135505 3138.116163 3140.156966 3147.115149 3153.1158375 3155.1314755 3156.151877 3210.1372985 3226.1322095 3228.1730125 3229.168249 3234.148536000001 3284.174072 3300.168983 3302.209786 3372.1901185 3374.2057565 3405.200342 3407.241145 3447.2472935 3448.24253 3448.267695 3503.248353 3517.227626 3519.268429 3520.2636655 3521.284067 3589.2487615 3591.2643995 3594.300439 3663.285535 3665.301173 3665.326338 3704.312085 3720.306996 3738.34271 3809.343444 3812.3794835 3827.353993 3866.364905 3882.359816 3886.416257 3959.432629</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	921 <token name="@MASS_OFFSET_GLYCO-O@">0 203.0794 365.1322 406.1588 494.1748 511.1901 527.185 568.2116 656.2276 673.2429 714.2695 730.2644 802.2855 818.2804 859.307 860.3274 876.3223 947.323 964.3383 1005.3649 1021.3598 1022.3802 1095.3966 1109.3758 1167.4177 1238.4184 1241.4545 1312.4552 1313.4756 1386.492 1387.5124 1441.4978 1458.5131 609.2382 697.2542 771.291 917.3489 933.3438 1062.3864 1063.4068 1079.4017 1150.4024 1208.4443 1224.4392 1225.4596 1298.476 1370.4971 1444.5339 1515.5346 1516.555 1589.5714 1590.5918 1644.5772 1661.5925 892.3172 1038.3751 1183.4126 1329.4705 1460.5288 1474.508 1532.5499 1603.5506 1606.5867 1677.5874 1678.6078 1751.6242 1752.6446 1806.63 1823.6453 812.3176 900.3336 974.3704 1120.4283 1136.4232 1265.4658 1266.4862 1282.4811 1353.4818 1411.5237 1427.5186 1428.539 1501.5554 1573.5765 1647.6133 1718.614 1719.6344 1792.6508 1793.6712 1847.6566 1864.6719 988.3496 1296.4603 1354.5022 1499.5397 1732.5932 1735.6293 1807.6504 1880.6668 1881.6872 1935.6726 1952.6879 1184.433 1371.5175 1475.5284 1533.5703 1620.5659 1749.6085 1824.6657 1897.6821 1898.7025 1969.7032 1054.37 1200.4279 1257.4494 1345.4654 1403.5073 1491.5233 1548.5448 1549.5652 1622.5816 1636.5608 1694.6027 1765.6034 1768.6395 1839.6402 1840.6606 1913.677 1914.6974 1968.6828 1985.6981 1663.6082 1809.6661 1954.7036 1955.724 2009.7094 2026.7247 1894.646 2042.7196 2043.74 2097.7254 2114.7407 1346.4858 1637.5812 1695.6231 1782.6187 1911.6613 1986.7185 2059.7349 2060.7553 2131.756 1574.5969 1736.6497 2027.7451 2100.7615 2101.7819 2155.7673 2172.7826 1825.661 1971.7189 2116.7564 2117.7768 2171.7622 2188.7775 1604.571 1662.6129 1766.6238 2040.7039 2115.7611 2189.7979 2243.7833 2260.7986 1927.6562 2056.6988 2130.7356 2204.7724 2205.7928 2259.7782 2276.7935 2245.799 2246.8194 2300.8048 2317.8201 1720.6548 1865.6923 1882.7076 2098.7458 2173.803 2247.8398 2301.8252 2318.8405 2262.8143 2263.8347 2334.8354 2185.7414 2333.815 2388.8208 2405.8361 1928.6766 2073.7141 2202.7567 2277.8139 2350.8303 2351.8507 2422.8514 2010.7298 2391.8569 2392.8773 2446.8627 2463.878 2407.8518 2408.8722 2462.8576 2479.8729 2044.7604 2335.8558 2409.8926 2480.8933 2190.7932 2336.8511 2481.8886 2482.909 2536.8944 2553.9097 2218.7516 2347.7942 2421.831 2495.8678 2496.8882 2550.8736 2567.8889 2554.9301 2608.9155 2625.9308 2476.8368 2551.894 2624.9104 2679.9162 2696.9315 2627.9465 2628.9669 2682.9523 2699.9676 2698.9472 2753.953 2770.9683 2626.9512 2700.988 2754.9734 2771.9887 2772.984 2774.0044 2827.9898 2845.0051 2775.0248 2829.0102 2846.0255 2882.9956 2900.0109 2917.0262 1015.397 1103.413 1177.4498 1323.5077 1339.5026 1468.5452 1469.5656 1485.5605 1556.5612 1614.6031 1630.598 1631.6184 1704.6348 1776.6559 1850.6927 1921.6934 1922.7138 1995.7302 1996.7506 2050.736 2067.7513 1191.429 1557.5816 1702.6191 1938.7087 2083.7462 2084.7666 2138.752 1866.6876 2012.7455 2157.783 2158.8034 2212.7888 2229.8041 1777.6763 1939.7291 2230.8245 2303.8409 2304.8613 2358.8467 2375.862 2028.7404 2174.7983 2319.8358 2320.8562 2374.8416 2448.8784 2449.8988 2503.8842 2520.8995 1923.7342 2068.7717 2085.787 2376.8824 2450.9192 2504.9046 2521.9199 2465.8937 2466.9141 2537.9148 2591.9002 2213.8092 2594.9363 2595.9567 2649.9421 2666.9574 2610.9312 2611.9516 2665.937 2538.9352 2612.972 2683.9727 2393.8726 2539.9305 2684.968 2685.9884 2739.9738 2756.9891 2758.0095 2811.9949 2831.0259 2832.0463 2886.0317 2903.047 2902.0266 2957.0324 2974.0477 2830.0306 2904.0674 2958.0528 2975.0681 2976.0634 2977.0838 2978.1042 1419.5022 1565.5601 1710.5976 1856.6555 1987.7138 2001.693 2133.7717 2278.8092 2279.8296 1711.618 2002.7134 2147.7509 2424.8671 2425.8875 2292.7884 2569.9046 2570.925 2641.9257 2293.8088 2438.8463 2642.9461 2715.9625 2716.9829 2787.9836 2555.9254 2701.9833 2847.0208 2848.0412 2919.0419 2583.8838 2712.9264 2786.9632 2861 2862.0204 2916.0058 2933.0211 2920.0623 2991.063 2841.969 2990.0426 2993.0787 2994.0991 2992.0834 1218.4764 1306.4924 1380.5292 1526.5871 1542.582 1671.6246 1672.645 1688.6399 1759.6406 1817.6825 1833.6774 1834.6978 1907.7142 1979.7353 2053.7721 2124.7728 2125.7932 2198.8096 2199.83 2253.8154 2270.8307 1394.5084 1760.661 1905.6985 2141.7881 2286.8256 2287.846 2341.8314 2069.767 2215.8249 2360.8624 2361.8828 2415.8682 2432.8835 1980.7557 2142.8085 2433.9039 2506.9203 2507.9407 2561.9261 2578.9414 2231.8198 2377.8777 2522.9152 2523.9356 2577.921 2651.9578 2652.9782 2706.9636 2723.9789 2126.8136 2271.8511 2288.8664 2579.9618 2653.9986 2707.984 2724.9993 2668.9731 2669.9935 2740.9942 2794.9796 2416.8886 2798.0157 2799.0361 2853.0215 2870.0368 2814.0106 2815.031 2869.0164 2742.0146 2816.0514 2887.0521 2596.952 2743.0099 2888.0474 2889.0678 2943.0532 2960.0685 2961.0889 1482.5244 1790.6351 1848.677 1993.7145 2226.768 2429.8474 2156.7877 2534.8787 2609.9359 2737.9581 2214.8296 2359.8671 2592.9206 2667.9778 2796 2813.0153 2941.0375 2971.0116 1857.6759 2148.7713 2206.8132 2497.9086 2571.9454 2231.8449 2393.8977 2684.9931 2759.0299 2439.8667 2584.9042 2713.9468 2789.004 2863.0408 2934.0415 2555.9505 2847.0459 2921.0827 2729.9417 2858.9843 2988.0269 1581.555 1727.6129 1784.6344 1872.6504 1930.6923 2018.7083 2075.7298 2076.7502 2149.7666 2163.7458 2221.7877 2295.8245 2366.8252 2367.8456 2440.862 2441.8824 2512.8831 1873.6708 2164.7662 2222.8081 2309.8037 2513.9035 2586.9199 2587.9403 2658.941 2352.846 2498.9039 2643.9414 2644.9618 2454.8412 2657.9206 2731.9574 2732.9778 2803.9785 2789.9993 2791.0197 2455.8616 2600.8991 2804.9989 2878.0153 2879.0357 2950.0364 2935.0368 2936.0572 2937.0776 2717.9782 2864.0361 2745.9366 2874.9792 2949.016 2759.0048 2905.0627 2019.7287 2310.8241 2368.866 2659.9614 2733.9982 2601.9195 2746.957 2875.9996 2951.0568 2718.0033 2891.9945 2434.9243 2596.9771 2888.0725 2962.1093 2921.0576 2406.8565 2464.8984 2568.9093 2842.9894 2918.0466 2522.9403 2901.0313 2976.0885 2730.9621 2580.9822 2726.0197 2743.035 2959.0732 2871.0572 2905.0878 2893.0149</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	922
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	923 <!-- Tokens used in the glyco_labiles section. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	924 <token name="@Y_TYPE_MASSES_LABILE_ADP-RIBOSYLATION@">0/114.03169/193.99802/291.97492/406.00661</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	925 <token name="@Y_TYPE_MASSES_NONSPECIFIC_HLA_GLYCO@">0 203.07937 406.15874 568.21156 730.26438 892.3172</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	926 <token name="@Y_TYPE_MASSES_GLYCO-N@">0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	927 <token name="@Y_TYPE_MASSES_GLYCO-O-HCD@">0 203.07937 365.1322</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	928 <token name="@Y_TYPE_MASSES_GLYCO-O-HYBRID@">0 203.07937 365.1322 406.15874 568.21156 730.26438 892.3172 349.137279</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	929 <token name="@Y_TYPE_MASSES_GLYCO-O-OPEN@">0 203.07937 406.15874 568.21156 730.26438 349.137279</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	930
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	931 <!-- Parameter 'ion_series_definitions' was not supplied. Using default value. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	932 <xml name="mass_offsets">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	933 <section name="mass_offsets" expanded="false" title="Mass Offsets">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	934 <param name="mass_offsets" type="select" label="Mass Offsets" help="glyco-N covers glyco-N-HCD, glyco-N-Hybrid, glyco-N-LFQ, glyco-N-TMT. glyco-O covers glyco-O-HCD, glyco-O-Hybrid, glyco-O-Pair">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	935 <option value="0" selected="true">None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	936 <option value="@MASS_OFFSET_MASS-OFFSET-COMMONPTMS@">Mass-Offset-CommonPTMs</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	937 <option value="@MASS_OFFSET_LABILE_ADP-RIBOSYLATION@">Labile_ADP-ribosylation: 0/541.06111</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	938 <option value="@MASS_OFFSET_LABILE_PHOSPHO@">Labile_phospho: 0/79.966331</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	939 <option value="@XRNAX-MASSOFFSET@">XRNAX-MassOffset</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	940 <option value="@FPOP@">FPOP</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	941 <option value="@MASS_OFFSET_GLYCO-N@">glyco-N</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	942 <option value="@MASS_OFFSET_GLYCO-O@">glyco-O</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	943 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	944 <param name="restrict_deltamass_to" type="select" label="Restrict deltamass to">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	945 <option value="all">All</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	946 <option value="STY">Labile_phospho: STY</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	947 <option value="ST-">glyco-O: ST-</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	948 <option value="SKREDTY">Labile_ADP-ribosylation: SKREDTY</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	949 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	950 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	951 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	952 <token name="@MASS_OFFSETS@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	953 #set $msfragger_dict['mass_offsets'] = $prefix.mass_offsets.mass_offsets
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	954 #set $msfragger_dict['restrict_deltamass_to'] = $prefix.mass_offsets.restrict_deltamass_to
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	955 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	956
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	957 <xml name="glyco_labile" token_diagnostic_intensity="0.0" token_min_sequence_matches="2">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	958 <section name="glyco_labile" expanded="false" title="Glyco/Labile Mods">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	959 <param name="labile_search_mode" type="select" label="Labile modification search mode">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	960 <option value="off">off</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	961 <option value="nglycan">nglycan</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	962 <option value="labile">labile</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	963 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	964 <param name="diagnostic_intensity_filter" type="float" value="@DIAGNOSTIC_INTENSITY@" min="0.0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	965 label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	966 <param name="min_sequence_matches" type="integer" value="@MIN_SEQUENCE_MATCHES@" min="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	967 label="Min Sequence-specific Ions" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	968 <param name="Y_type_masses" type="select" label="Y ion masses" help="glyco-N covers glyco-N-HCD, glyco-N-Hybrid, glyco-N-LFQ, glyco-N-TMT, glyco-N-open-HCD, glyco-N-open-Hybrid">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	969 <option value="" selected="true">None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	970 <option value="@Y_TYPE_MASSES_LABILE_ADP-RIBOSYLATION@">Labile_ADP-ribosylation</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	971 <option value="@Y_TYPE_MASSES_NONSPECIFIC_HLA_GLYCO@">Nonspecific-HLA-glyco</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	972 <option value="@Y_TYPE_MASSES_GLYCO-N@">glyco-N</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	973 <option value="@Y_TYPE_MASSES_GLYCO-O-HCD@">glyco-O-HCD</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	974 <option value="@Y_TYPE_MASSES_GLYCO-O-HYBRID@">glyco-O-Hybrid</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	975 <option value="@Y_TYPE_MASSES_GLYCO-O-OPEN@">glyco-O-open-HCD,glyco-O-open-Hybrid</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	976 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	977 <param name="diagnostic_fragments" type="select" label="Diagnostic fragment masses">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	978 <option value="">None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	979 <option value="136.06232/250.09401/348.07036/428.03669/584.09018">Labile_ADP-ribosylation: 136.06232/250.09401/348.07036/428.03669/584.09018</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	980 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	981 <param name="remainder_fragment_masses" type="text" optional="true" label="Remainder fragment masses"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	982 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	983 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	984 <token name="@GLYCO_LABILE@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	985 #set $msfragger_dict['labile_search_mode'] = $prefix.glyco_labile.labile_search_mode
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	986 #if $prefix.glyco_labile.labile_search_mode != 'off'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	987 #set $msfragger_dict['diagnostic_intensity_filter'] = $prefix.glyco_labile.diagnostic_intensity_filter
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	988 #set $msfragger_dict['min_sequence_matches'] = $prefix.glyco_labile.min_sequence_matches
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	989 #set $msfragger_dict['diagnostic_fragments'] = $prefix.glyco_labile.diagnostic_fragments
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	990
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	991 #if $prefix.glyco_labile.remainder_fragment_masses != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	992 #set $msfragger_dict['remainder_fragment_masses'] = $prefix.glyco_labile.remainder_fragment_masses
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	993 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	994 #set $msfragger_dict['Y_type_masses'] = $prefix.glyco_labile.Y_type_masses
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	995 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	996 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	997
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	998 <!-- Formatting options for output files. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	999 <xml name="advanced_options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1000 <section name="advanced_options" expanded="false" title="Advanced Options">
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	1001 <param name="output_format" type="select" label="output format">
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1002 <option value="pepXML">PEPXML</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1003 <option value="tsv">TSV</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1004 <option value="tsv_pepXML">TSV_PEPXML</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1005 <option value="pin">PIN</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1006 <option value="tsv_pin">TSV_PIN</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1007 <option value="pepXML_pin" selected="true">PEPXML_PIN</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1008 <option value="tsv_pepXML_pin">TSV_PEPXML_PIN</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1009 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1010 <param name="output_report_topN" type="integer" value="1" min="1" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1011 label="Reports top N PSMs per input spectrum Default:1" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1012 <param name="report_alternative_proteins" type="boolean" checked="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1013 label="Report alternative proteins"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1014 <param name="output_max_expect" type="float" value="50.0" min="0.0" optional="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1015 label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1016
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1017 <param name="write_calibrated_mzml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write calibrated mzML"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1018 <param name="group_variable" type="select" optional="true" label="Group variable">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1019 <option value="0">None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1020 <option value="1">Number of enzymatic termini</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1021 <option value="2">Protein evidence from FASTA file</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1022 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1023 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1024 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1025
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1026 <!-- Does not enter into msfragger_dict, instead produces configuration text. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1027 <token name="@MSFRAGGER_ADVANCED_OPTIONS@"><![CDATA[
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	1028 #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	1029 #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1030 #set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins
7 b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4 galaxyp parents: 6 diff changeset	1031 #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1032 #if $prefix.advanced_options.output_max_expect != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1033 #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1034 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1035 #set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1036 #if $prefix.advanced_options.group_variable != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1037 #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1038 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1039 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1040
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1041 <!-- Composes all parameter tokens for generating msfragger_dict for -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1042 <token name="@MSFRAGGER_PARAM_DICT@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1043 #import re
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1044 #set $msfragger_dict = {}
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1045 @SEARCH_TOLERANCES@
5 e06c94fe89cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 1dd092b0008017e57b66775f1763f824d100ca08 galaxyp parents: 0 diff changeset	1046 @DIGESTION@
0 41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1047 ## Variable Modification Parameters sets $vmods
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1048 @VARIABLE_MODIFICATION@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1049 ## Static Modification Parameters sets $fmods
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1050 @STATIC_MODIFICATION@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1051 @GLYCO_LABILE@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1052 @MASS_OFFSETS@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1053 @SPECTRUM_PROCESSING@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1054 @OPEN_SEARCH@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1055 @MODELING_OUTPUT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1056 @MSFRAGGER_ADVANCED_OPTIONS@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1057 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1058 </macros>

Mercurial > repos > galaxyp > fragpipe

annotate msfragger_macros.xml @ 7:b4f6df8fa89b draft