Mercurial > repos > jjohnson > encyclopedia_walnut

annotate macros.xml @ 9:886a93db834d draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 7a9a7f310631cb909bb4e55c5d8541b39071fc81"
author jjohnson
date Thu, 10 Sep 2020 21:37:17 +0000
parents c0af2ce65e32
children
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rev   line source
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1 <macros>
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2 <token name="@VERSION@">0.9.5</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
2
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9
1
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10 <token name="@ENCYCLOPEDIA_WIKI@">
9
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11 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home
1
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12
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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14 </token>
0
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15 <xml name="citations">
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16 <citations>
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17 <citation type="doi">10.1038/s41467-018-07454-w</citation>
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18 <citation type="doi">10.1038/s41467-020-15346-1</citation>
1
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19 <citation type="doi">10.1074/mcp.P119.001913</citation>
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20 <yield/>
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21 </citations>
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22 </xml>
2
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23
0
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24 <token name="@CMD_IMPORTS@">
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25 #import re
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26 #def identifier_or_name($input1)
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27 #if hasattr($input1, 'element_identifier')
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28 #return $input1.element_identifier
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29 #else
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30 #return $input1.name
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31 #end if
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32 #end def
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33 #def clean($name1)
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34 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
0
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35 #return $name_clean
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36 #end def
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37 #def ln_name($ds)
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38 #set $ext = ''
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39 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
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40 #set $ext = ".mzML"
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41 #else if $ds.is_of_type('elib')
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42 #set $ext = ".elib"
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43 #else if $ds.is_of_type('dlib')
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44 #set $ext = ".dlib"
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45 #else if $ds.is_of_type('blib')
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46 #set $ext = ".blib"
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47 #else if $ds.is_of_type('fasta')
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48 #set $ext = ".fasta"
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49 #else if $ds.is_of_type('fasta.gz')
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50 #set $ext = ".fasta.gz"
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51 #end if
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52 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
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53 #return $name
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54 #end def
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55 #set $i_name = None
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56 #set $f_name = None
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57 #set $l_name = None
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58 #set $t_name = None
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59 </token>
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60
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61 <xml name="scan_input">
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62 <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
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63 <help>@MSCONVERT_RAW@</help>
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64 </param>
0
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65 </xml>
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66 <token name="@LINK_SCAN_INPUT@"><![CDATA[
5
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67 #set $i_name = $ln_name($scan_input)
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68 ln -s '$scan_input' '$i_name' &&
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69 ]]></token>
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70 <token name="@SCAN_INPUT@">
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71 -i '$i_name'
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72 </token>
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73
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74 <xml name="scan_inputs">
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75 <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
1
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76 <help>@MSCONVERT_RAW@</help>
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77 </param>
0
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78 </xml>
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79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
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80 #set $inputs_dir = 'inputs'
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81 mkdir -p $inputs_dir &&
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82 #for $sf in $scan_inputs
0
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83 #set $i_name = $ln_name($sf)
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84 ln -s '$sf' '${inputs_dir}/${i_name}' &&
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85 #end for
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86 ]]></token>
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87 <token name="@SCAN_INPUTS@">
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88 -i '$inputs_dir'
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89 </token>
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90
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91 <xml name="fasta_input">
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92 <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
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93 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
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94 </param>
0
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95 </xml>
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96 <token name="@LINK_FASTA_INPUT@"><![CDATA[
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97 #set $f_name = $ln_name($fasta)
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98 ln -s '$fasta' '$f_name' &&
0
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99 ]]></token>
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100 <token name="@FASTA_INPUT@">
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101 -f '$f_name'
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102 </token>
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103
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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104 <xml name="target_fasta">
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105 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true">
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106 <help>Optional - Only analyze this subset of the background fasta proteome</help>
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107 </param>
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108 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides">
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109 <help>Rather than full proteins</help>
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110 </param>
0
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111 </xml>
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112 <token name="@LINK_TARGET_FASTA@"><![CDATA[
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113 #if $target_fasta
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114 #set $t_name = $ln_name($target_fasta)
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115 ln -s '$target_fasta' '$t_name' &&
0
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116 #else
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117 #set $t_name = None
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118 #end if
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119 ]]></token>
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120 <token name="@TARGET_FASTA@">
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121 #if $t_name
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122 -t '$t_name'
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123 -tp $tp
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124 #end if
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125 </token>
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126
1
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127 <xml name="lib_input" token_optional="true" token_libhelp="">
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128 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
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129 <help>@LIBHELP@</help>
0
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130 </param>
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131 </xml>
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132 <token name="@LINK_LIB_INPUT@"><![CDATA[
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133 #if $library
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134 #set $l_name = $ln_name($library)
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135 cp '$library' '$l_name' &&
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136 #else
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137 #set $l_name = None
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138 #end if
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139 ]]></token>
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140 <token name="@LIB_INPUT@">
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141 #if $l_name
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142 -l '$l_name'
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143 #end if
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144 </token>
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145
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146 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false"
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147 token_cid_selected="false" token_hcd_selected="false">
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148 <conditional name="acquisition">
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149 <param name="set_acquisition" type="select" label="Set Acquisition Options">
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150 <option value="no">No - use default options</option>
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151 <option value="yes">Yes</option>
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152 </param>
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153 <when value="no"/>
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154 <when value="yes">
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155 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
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156 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type">
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157 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option>
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158 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option>
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159 </param>
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160 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
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161 <option value="Trypsin">Trypsin</option>
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162 <option value="Trypsin/p">Trypsin/p</option>
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163 <option value="Lys-C">Lys-C</option>
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164 <option value="Lys-N">Lys-N</option>
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165 <option value="Arg-C">Arg-C</option>
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166 <option value="Glu-C">Glu-C</option>
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167 <option value="Chymotrypsin">Chymotrypsin</option>
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168 <option value="Pepsin A">Pepsin A</option>
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169 <option value="Elastase">Elastase</option>
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170 <option value="Thermolysin">Thermolysin</option>
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171 <option value="No Enzyme">No Enzyme</option>
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172 </param>
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173 <param argument="-frag" type="select" optional="true" label="Fragmentation">
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174 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option>
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175 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option>
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176 <option value="ETD">ETD (C/Z/Z+1)</option>
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177 </param>
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178 </when>
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179 </conditional>
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180 </xml>
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181 <xml name="encyclopedia_common_options">
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182 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false"
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183 token_cid_selected="true" token_hcd_selected="false"/>
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184 </xml>
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185 <xml name="walnut_common_options">
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186 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
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187 token_cid_selected="false" token_hcd_selected="true"/>
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188 </xml>
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189 <token name="@COMMON_OPTIONS@">
2
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190 #if $options.acquisition.set_acquisition == 'yes'
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191 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
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192 #if $options.acquisition.acquisition
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193 -acquisition '$options.acquisition.acquisition'
0
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194 #end if
2
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195 #if $options.acquisition.enzyme:
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196 -enzyme '$options.acquisition.enzyme'
0
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197 #end if
2
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198 #if $options.acquisition.frag:
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199 -frag '$options.acquisition.frag'
0
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200 #end if
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201 #end if
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202 </token>
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203
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204 <xml name="mass_tolerance">
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205 <conditional name="tolerance">
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206 <param name="set_tolerance" type="select" label="Set Tolerance Options">
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207 <option value="no">No - use default options</option>
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208 <option value="yes">Yes</option>
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209 </param>
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210 <when value="no"/>
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211 <when value="yes">
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212 <conditional name="precursor_tolerance">
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213 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
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214 <option value="PPM">PPM</option>
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215 <option value="AMU">AMU</option>
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216 <option value="Resolution">Resolution</option>
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217 </param>
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218 <when value="PPM">
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219 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
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220 </when>
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221 <when value="AMU">
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222 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
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223 </when>
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224 <when value="Resolution">
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225 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
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226 </when>
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227 </conditional>
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228 <conditional name="fragment_tolerance">
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229 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
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230 <option value="PPM">PPM</option>
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231 <option value="AMU">AMU</option>
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232 <option value="Resolution">Resolution</option>
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233 </param>
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234 <when value="PPM">
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235 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
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236 </when>
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237 <when value="AMU">
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238 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
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239 </when>
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240 <when value="Resolution">
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241 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
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242 </when>
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243 </conditional>
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244 <yield/>
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245 </when>
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246 </conditional>
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247 </xml>
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248 <token name="@MASS_TOLERANCE@">
2
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249 #if $options.tolerance.set_tolerance == 'yes'
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250 -ptolunits $options.tolerance.precursor_tolerance.ptolunits
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251 -ptol $options.tolerance.precursor_tolerance.ptol
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252 -ftolunits $options.tolerance.fragment_tolerance.ftolunits
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253 -ftol $options.tolerance.fragment_tolerance.ftol
0
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254 #end if
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255 </token>
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256
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257 <xml name="mass_library_tolerance">
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258 <expand macro="mass_tolerance">
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259 <conditional name="library_tolerance">
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260 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
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261 <option value="defaults">Use defaults</option>
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262 <option value="PPM">PPM</option>
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263 <option value="AMU">AMU</option>
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264 <option value="Resolution">Resolution</option>
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265 </param>
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266 <when value="defaults"/>
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267 <when value="PPM">
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268 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
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269 </when>
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270 <when value="AMU">
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271 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
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272 </when>
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273 <when value="Resolution">
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274 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
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275 </when>
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276 </conditional>
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277 </expand>
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278 </xml>
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279 <token name="@MASS_LIBRARY_TOLERANCE@">
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280 @MASS_TOLERANCE@
2
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281 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
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282 -ltolunits $options.tolerance.library_tolerance.ltolunits
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283 -ltol $options.tolerance.library_tolerance.ltol
0
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284 #end if
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285 </token>
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286
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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287 <xml name="percolator_options">
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288 <conditional name="percolator">
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289 <param name="set_percolator" type="select" label="Set Percolator Options">
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290 <option value="no">No - use default options</option>
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291 <option value="yes">Yes</option>
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292 </param>
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293 <when value="no"/>
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294 <when value="yes">
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295 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
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296 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
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297 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
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298 </when>
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299 </conditional>
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300 </xml>
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301 <token name="@PERCOLATOR_OPTIONS@">
2
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302 #if $options.percolator.set_percolator == 'yes'
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303 #if str($options.percolator.percolatorVersionNumber)
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304 -percolatorVersionNumber $options.percolator.percolatorVersionNumber
0
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305 #end if
2
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306 #if str($options.percolator.percolatorProteinThreshold)
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307 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
0
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308 #end if
2
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309 #if str($options.percolator.percolatorThreshold)
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310 -percolatorThreshold $options.percolator.percolatorThreshold
0
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311 #end if
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312 #end if
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313 </token>
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314
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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315 <xml name="peak_options">
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316 <conditional name="peak">
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317 <param name="set_peak" type="select" label="Set Peak Options">
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318 <option value="no">No - use default options</option>
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319 <option value="yes">Yes</option>
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320 </param>
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321 <when value="no"/>
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322 <when value="yes">
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323 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/>
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324 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/>
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325 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/>
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diff changeset
326 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
327 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
328 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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diff changeset
329 <option value="false">No</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
330 <option value="true">Yes</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
331 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
332 </when>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
333 </conditional>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
334 </xml>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
335 <token name="@PEAK_OPTIONS@">
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
336 #if $options.peak.set_peak == 'yes'
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
337 #if str($options.peak.numberOfQuantitativePeaks)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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338 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
339 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
340 #if str($options.peak.minNumOfQuantitativePeaks)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
341 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
342 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
343 #if str($options.peak.minQuantitativeIonNumber)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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344 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
345 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
346 #if str($options.peak.minIntensity)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
347 -minIntensity $options.peak.minIntensity
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
348 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
349 #if str($options.peak.expectedPeakWidth)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
350 -expectedPeakWidth $options.peak.expectedPeakWidth
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
351 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
352 #if $options.peak.filterPeaklists
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
353 -filterPeaklists $options.peak.filterPeaklists
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
354 #end if
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
355 #end if
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
356 </token>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
357
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
358 <xml name="window_options">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
359 <conditional name="window">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
360 <param name="set_window" type="select" label="Set Window Options">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
361 <option value="no">No - use default options</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
362 <option value="yes">Yes</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
363 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
364 <when value="no"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
365 <when value="yes">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
366 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
367 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
368 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
369 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
370 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
371 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
372 <option value="window">Across entire window</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
373 <option value="recal20">Recalibrated (20% gradient)</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
374 <option value="recal">Recalibrated (peak width only)</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
375 <option value="uncal20">Uncalibrated (20% gradient)</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
376 <option value="uncal">Uncalibrated (peak width only)</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
377 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
378 </when>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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diff changeset
379 </conditional>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
380 </xml>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
381 <token name="@WINDOW_OPTIONS@">
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
382 #if $options.window.set_window == 'yes'
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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383 #if str($options.window.foffset)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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384 -foffset $options.window.foffset
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
385 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
386 #if str($options.window.poffset)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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387 -poffset $options.window.poffset
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
388 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
389 #if str($options.window.precursorIsolationMargin)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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390 -precursorIsolationMargin $options.window.precursorIsolationMargin
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
391 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
392 #if str($options.window.precursorWindowSize)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
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393 -precursorWindowSize $options.window.precursorWindowSize
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
394 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
395 #if str($options.window.rtWindowInMin)
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
396 -rtWindowInMin $options.window.rtWindowInMin
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
397 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
398 #if $options.window.scoringBreadthType
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
399 -scoringBreadthType $options.window.scoringBreadthType
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
400 #end if
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
401 #end if
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
402 </token>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
403
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
404 <xml name="modification_options">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
405 <conditional name="modifications">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
406 <param name="set_modifications" type="select" label="Set Modifications Options">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
407 <option value="no">No - use default options</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
408 <option value="yes">Yes</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
409 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
410 <when value="no"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
411 <when value="yes">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
412 <param argument="-fixed" type="select" optional="true" label="Fixed Modification">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
413 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
414 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
415 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
416 <option value="C=125.047679">C+125 (NEM) C=125.047679</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
417 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
418 <yield/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
419 <!--
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
420 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
421 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
422 -->
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
423 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
424 </when>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
425 </conditional>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
426 </xml>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
427 <token name="@MODIFICATION_OPTIONS@">
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
428 #if $options.modifications.set_modifications == 'yes'
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
429 #if $options.modifications.fixed
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
430 -fixed $options.modifications.fixed
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
431 #end if
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
432 -verifyModificationIons $options.modifications.verifyModificationIons
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
433 #end if
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
434 </token>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
435
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
436 <xml name="search_options">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
437 <conditional name="search">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
438 <param name="set_search" type="select" label="Set Search Options">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
439 <option value="no">No - use default options</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
440 <option value="yes">Yes</option>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
441 </param>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
442 <when value="no"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
443 <when value="yes">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
444 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
445 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
446 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
447 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
448 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
449 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
450 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
451 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
452 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
453 <!--
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
454 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
455 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
456 -->
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
457 </when>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
458 </conditional>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
459 </xml>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
460 <token name="@SEARCH_OPTIONS@">
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
461 #if $options.search.set_search == 'yes'
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
462 -minCharge $options.search.minCharge
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
463 -maxCharge $options.search.maxCharge
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
464 -minLength $options.search.minLength
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
465 -maxLength $options.search.maxLength
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
466 -minEluteTime $options.search.minEluteTime
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
467 -maxMissedCleavage $options.search.maxMissedCleavage
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
468 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
469 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
470 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
471 ## -addDecoysToBackground $options.search.addDecoysToBackground
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
472 ## -dontRunDecoys $options.search.dontRunDecoys
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
473 #end if
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
parents:
diff changeset
474 </token>
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
475
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
476 <xml name="options_section">
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
477 <section name="options" title="Parameter Settings" expanded="false">
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
478 <expand macro="common_options"/>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
479 <expand macro="mass_library_tolerance"/>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
480 <expand macro="percolator_options"/>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
481 <expand macro="peak_options"/>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
482 <expand macro="window_options"/>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
483 <expand macro="modification_options"/>
3
e37e3c4a87a9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"
jjohnson
parents: 2
diff changeset
484 <expand macro="search_options"/>
2
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 1
diff changeset
485 </section>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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486 </xml>
114b44e35d30 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
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487
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
jjohnson
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488 <xml name="libexport">
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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489 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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490 </xml>
1
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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491 <token name="@MSCONVERT_CMD@"><![CDATA[
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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492 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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493 ]]>
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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494 </token>
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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495 <token name="@MSCONVERT_RAW@"><![CDATA[
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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496 mzML conversion from RAW requires special options: @MSCONVERT_CMD@
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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497 ]]>
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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498 </token>
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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499 <token name="@MSCONVERT_HELP@"><![CDATA[
0
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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500
6
0172dfa08216 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
jjohnson
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501 The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:
1
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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502
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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503 ::
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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504
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
jjohnson
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505 @MSCONVERT_CMD@
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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506
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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507 ]]>
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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508 </token>
6635b68da948 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
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509 </macros>