annotate moff.xml @ 5:a96af68dafb2 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52"
author galaxyp
date Wed, 06 May 2020 14:50:08 -0400
parents 7af419c90f5f
children
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7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c
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1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.0">
0
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2 <description>extracts MS1 intensities from spectrum files</description>
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3 <macros>
5
a96af68dafb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52"
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4 <token name="@VERSION@">2.0.3</token>
0
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5 <!-- xml macros, used for shared Galaxy parameter inputs -->
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6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data">
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7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff -->
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8 <conditional name="ident_input">
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9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:">
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10 <option value="ps">Peptide Shaker PSM report (standard, not extended)</option>
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11 <option value="generic">Another tabular identification file</option>
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12 </param>
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13 <when value="ps">
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14 <param name="ident_input_file" type="@INPUT_TYPE@" format="tabular" label="Peptide Shaker PSM report" multiple="@ALLOW_MULTIPLE@"/>
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15 </when>
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16 <when value="generic">
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17 <param name="ident_input_file" type="@INPUT_TYPE@" format="tabular" label="A general tabular format" multiple="@ALLOW_MULTIPLE@"
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18 help="Must have specific columns; see below to select these columns from your file. The file should have at most one header line. "/>
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19 <param name="remove_header" type="boolean" value="false" label="Remove the header line?" help="This is necessary if the file has a line with column headers"/>
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20 <param name="peptide"
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21 type="data_column"
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22 data_ref="ident_input_file"
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23 label="Column with peptide-spectrum-match sequence"/>
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24 <param name="prot"
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25 type="data_column"
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26 data_ref="ident_input_file"
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27 label="Column with protein ID"/>
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28 <param name="mod_peptide"
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29 type="data_column"
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30 data_ref="ident_input_file"
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31 label="Column with peptide-spectrum-match sequence that contains possible modifications"/>
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32 <param name="rt"
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33 type="data_column"
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34 data_ref="ident_input_file"
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35 label="Column with PSM retention time (in second)"/>
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36 <param name="mz"
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37 type="data_column"
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38 data_ref="ident_input_file"
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39 label="Column with m/z (mass over charge)"/>
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40 <param name="mass"
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41 type="data_column"
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42 data_ref="ident_input_file"
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43 label="Column with mass of the peptide"/>
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44 <param name="charge"
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45 type="data_column"
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46 data_ref="ident_input_file"
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47 label="Column with charge of ionized peptide"/>
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48 </when>
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49 </conditional>
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50 </xml>
4
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51 <xml name="filt_matched_peptide">
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52 <conditional name="match_filter">
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53 <param name="filter_flags" type="select" label="Activate filtering of matched peptides">
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54 <option selected="True" value="nofilter">Do not activate</option>
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55 <option value="filter">Filter by flags to exclude or require</option>
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56 </param>
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57 <when value="filter">
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58 <param argument="--sample_size" label="sample_size" type="float" value="0.20" help="percentage of MS2 peptide used to estimated the threshold. Default value: 0.20" />
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59 <param argument="--quantile_thr_filtering" label="-quantile_thr_filtering" type="float" value="0.75" help="quantile value used to compute the filtering threshold for the matched peak"/>
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60 <param argument="--ptm_file" type="data" format="tabular" label="ptm_file" optional= "True" help="load your ptm file in order to overwrite internal method"/>
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61 </when>
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62 <when value="nofilter"/>
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63 </conditional>
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64 </xml>
0
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65 <!-- tokens (code snippets used in <command>) -->
3
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66 <token name="@FORMAT@"><![CDATA[
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67 #if $task.task_selector != 'mbr'
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68 #if $task.msms_input.input_type_selector == "raw":
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69 #set $format = '.raw'
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70 #else
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71 #set $format = '.mzml'
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72 #end if
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73 #else:
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74 #set $format = '.tabular'
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75 #end if
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76 ]]></token>
0
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77 <token name="@IDENT_INPUT_ARG_MULTIPLE@"><![CDATA[
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78 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
4
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79 --tsv_list
3
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80 #for $value in $task.ident_input.ident_input_file:
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81 './ident_inputs/$value.element_identifier$format'
0
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82 #end for
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83 ]]></token>
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84 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[
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85 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
4
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86 --tsv_list './ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format'
0
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87 ]]></token>
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88 <token name="@WRANGLE_IDENT_INPUT_SINGLE@"><![CDATA[
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89 mkdir ./ident_inputs &&
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90 #if $task.ident_input.input_type_selector == "ps":
3
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91 cp '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
0
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92 #else
2
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93 cp '$task.ident_input.ident_input_file' ./tempfile1.tab &&
0
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94 ## optionally remove first line
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95 #if $task.ident_input.remove_header:
2
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96 sed -i '1d' ./tempfile1.tab &&
0
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97 #end if
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98 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
2
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99 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > ./tempfile2.tab &&
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100 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" ./tempfile1.tab >> ./tempfile2.tab &&
3
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101 mv ./tempfile2.tab './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
0
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102 #end if
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103 ]]></token>
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104 <token name="@WRANGLE_IDENT_INPUT_MULTIPLE@"><![CDATA[
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105 mkdir ./ident_inputs &&
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106 #if $task.ident_input.input_type_selector == "ps":
3
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107 #for $value in $task.ident_input.ident_input_file:
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108 cp '${value}' './ident_inputs/${value.element_identifier}$format' &&
0
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109 #end for
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110 #else
3
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111 #for $i, $value in enumerate($task.ident_input.ident_input_file):
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112 cp '${value}' './tempfile${i}_1.tab' &&
0
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113 ## optionally remove first line
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114 #if $task.ident_input.remove_header:
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115 sed -i '1d' './tempfile${i}_1.tab' &&
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116 #end if
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117 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
3
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118 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > './tempfile${i}_2.tab' &&
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119 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" './tempfile${i}_1.tab' >> './tempfile${i}_2.tab' &&
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120 mv './tempfile${i}_2.tab' './ident_inputs/${value.element_identifier}$format' &&
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121 #end for
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122 #end if
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123 ]]></token>
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124 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[
4
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125 --raw_list './raws/$task.msms_input.raw_list.element_identifier$format'
0
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126 ]]></token>
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127 <token name="@RAW_INPUT_ARG_MULTIPLE@"><![CDATA[
4
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128 --raw_list
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129 #for $value in $task.msms_input.raw_list:
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130 './raws/$value.element_identifier$format'
0
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131 #end for
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132 ]]></token>
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133 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[
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134 mkdir ./raws &&
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135 ## for files, need to softlink the name to the history item
4
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136 ln -s '$task.msms_input.raw_list' './raws/$task.msms_input.raw_list.element_identifier$format' &&
0
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137 ]]></token>
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138 <token name="@WRANGLE_RAW_INPUT_MULTIPLE@"><![CDATA[
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139 mkdir ./raws &&
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140 ## for files, need to softlink the name to the history item
4
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141 #for $value in $task.msms_input.raw_list:
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142 ln -s '$value' './raws/$value.element_identifier$format' &&
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143 #end for
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144 ]]></token>
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145 </macros>
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146 <requirements>
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147 <requirement type="package" version="@VERSION@">moff</requirement>
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148 </requirements>
2
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149 <version_command>echo @VERSION@</version_command>
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150 <command detect_errors="aggressive"><![CDATA[
3
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151 @FORMAT@
0
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152 mkdir ./out &&
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153 #if $task.task_selector == "moff":
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154 @WRANGLE_IDENT_INPUT_SINGLE@
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155 @WRANGLE_RAW_INPUT_SINGLE@
4
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156 moff_all.py
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157 @IDENT_INPUT_ARG_SINGLE@
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158 @RAW_INPUT_ARG_SINGLE@
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159 --tol $task.tol
4
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160 --mbr $task.mbr
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161 --xic_length $task.xic_length
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162 --rt_peak_win $task.rt_peak_win
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163 --rt_peak_win_match $task.rt_peak_win_match
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164 --loc_out ./out
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165 #if str( $task.match_filter.filter_flags ) == "filter":
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166 --match_filter
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167 --sample_size $task.match_filter.sample_size
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168 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
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169 #if ($task.match_filter.ptm_file):
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170 --ptm_file '$task.match_filter.ptm_file'
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171 #else:
5
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172 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
4
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173 #end if
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174 #end if
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175 #if ($task.peptide_summary):
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176 --peptide_summary
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177 #end if
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178 #if $task.peptide_summary:
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179 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
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180 #end if
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181 &&
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182 mv ./out/*moff_result.txt '$output_table'
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183 &&
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184 mv ./out/*.log '$output_logs'
0
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185 #else if $task.task_selector == "mbr":
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186 @WRANGLE_IDENT_INPUT_MULTIPLE@
4
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187 moff_all.py
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188 @IDENT_INPUT_ARG_MULTIPLE@
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189 --mbr $task.mbr
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190 --raw_list
0
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191 &&
4
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192 mv ./mbr_output/* ./out
0
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193 #else:
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194 ## moff_all (mbr followed by apex)
4
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195 @WRANGLE_IDENT_INPUT_SINGLE@
0
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196 @WRANGLE_RAW_INPUT_MULTIPLE@
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197 moff_all.py
4
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198 @IDENT_INPUT_ARG_SINGLE@
0
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199 @RAW_INPUT_ARG_MULTIPLE@
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200 --tol $task.tol
4
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201 --mbr $task.mbr
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202 --xic_length $task.xic_length
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203 --rt_peak_win $task.rt_peak_win
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204 --rt_peak_win_match $task.rt_peak_win_match
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205 --loc_out ./out
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206 #if ($task.peptide_summary):
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207 --peptide_summary
0
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208 #end if
4
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209 #if str( $task.match_filter.filter_flags ) == "filter":
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210 --match_filter
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211 --sample_size $task.match_filter.sample_size
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212 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
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213 #if ($task.match_filter.ptm_file):
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214 --ptm_file '$task.match_filter.ptm_file'
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215 #else:
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216 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
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217 #end if
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218 #end if
5
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219
0
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220 #if $task.peptide_summary:
4
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221 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
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222 #end if
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223 #end if
0
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224 ]]></command>
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225 <inputs>
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226 <conditional name="task">
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227 <param name="task_selector" type="select" label="Choose which module to run">
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228 <option value="moff">Apex intensity</option>
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229 <option value="mbr">Match between runs</option>
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230 <option value="all">All (match-between-runs followed by quantitation)</option>
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231 </param>
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232 <when value = "moff">
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233 <expand macro="ident_input_macro" allow_multiple="false"/>
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234 <conditional name="msms_input">
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235 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
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236 <option value="raw">Thermo RAW file</option>
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237 <option value="mzml">mzML</option>
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238 </param>
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239 <when value="raw">
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240 <param argument="--raw_list" type="data" multiple="false" format="thermo.raw" label="RAW file(s)"/>
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241 </when>
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242 <when value="mzml">
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243 <param argument="--raw_list" type="data" multiple="false" format="mzml" label="mzML file(s)"/>
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244 </when>
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245 </conditional>
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246
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247
0
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248 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
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249 help="Specify the tolerance parameter in ppm." />
4
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250 <param argument="--mbr" type="text" value="off" label="moFF workflow"
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251 help="select the moFF workflow" />
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252 <param argument="--xic_length" type="float" value="3.0" label="retention time windows for XiC"
0
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253 help="Specify rt window for xic in minutes." />
4
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254 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
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255 help="Specify rt window for the peak in minutes." />
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256 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
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257 help="Specify the retention time window for the matched peak in minutes." />
5
a96af68dafb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52"
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258 <expand macro="filt_matched_peptide"/>
0
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259 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
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260 </when>
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261 <when value="mbr">
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262 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
4
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263 <param argument="--mbr" type="text" value="only" label="moFF workflow"
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264 help="select the moFF workflow" />
0
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265 </when>
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266 <when value="all">
4
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267 <expand macro="ident_input_macro" allow_multiple="false" input_type="data"/>
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268 <conditional name="msms_input">
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269 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
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270 <option value="raw">Thermo RAW file</option>
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271 <option value="mzml">mzML</option>
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272 </param>
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273 <when value="raw">
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274 <param argument="--raw_list" type="data" multiple="true" min="2" format="thermo.raw" label="RAW file(s)"/>
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275 </when>
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276 <when value="mzml">
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277 <param argument="--raw_list" type="data" multiple="true" min="2" format="mzml" label="mzML file(s)"/>
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278 </when>
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279 </conditional>
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280
0
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281 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
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282 help="Specify the tolerance parameter in ppm." />
4
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283 <param argument="--mbr" type="text" value="on" label="moFF workflow"
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284 help="select the moFF workflow" />
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285 <param argument="--xic_length" type="float" value="3.0" label="retention time windows for XiC"
0
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286 help="Specify rt window for xic in minutes." />
4
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287 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
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288 help="Specify the retention time window for the peak in minutes." />
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289 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
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290 help="Specify the retention time window for the matched peak in minutes." />
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291 <expand macro="filt_matched_peptide"/>
0
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292 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
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293 </when>
4
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294 </conditional>
0
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295 </inputs>
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296 <outputs>
2
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297 <data format="tabular" name="output_table" label="${tool.name} on ${on_string}: quantification">
0
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298 <filter>task['task_selector']=='moff'</filter>
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299 </data>
2
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300 <data format="txt" name="output_logs" label="${tool.name} ${on_string}: log">
0
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301 <filter>task['task_selector']=='moff'</filter>
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302 </data>
2
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303 <collection name="ident_output" type="list" label="${tool.name} on ${on_string}: quantification">
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304 <filter>task['task_selector']=='all'</filter>
0
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305 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.txt" directory="out" format="tabular"/>
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306 </collection>
2
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307 <collection name="ident_output_mbr" type="list" label="${tool.name} on ${on_string}: matched">
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308 <filter>task['task_selector']=='mbr'</filter>
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309 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.txt" directory="out" format="tabular"/>
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310 </collection>
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311 <collection name="log_output" type="list" label="${tool.name} on ${on_string}: logs">
0
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312 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
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313 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.log" directory="out" format="txt"/>
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314 </collection>
2
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315 <data format="tabular" name="output_peptide_summary" label="${tool.name} on ${on_string}: peptide summary">
4
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316 <filter>(task['task_selector']=='all' or task['task_selector']=='moff') and task['peptide_summary'] </filter>
0
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317 </data>
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318 </outputs>
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319 <tests>
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320 <!-- test mbr -->
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321 <test>
2
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322 <param name="task|task_selector" value="mbr"/>
1
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323 <param name="ident_input|input_type_selector" value="ps"/>
0
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324 <param name="ident_input_file">
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325 <collection type="list">
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326 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
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327 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
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328 </collection>
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329 </param>
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330 <param name="ext" value="tabular"/>
2
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331 <output_collection name="ident_output_mbr" type="list" count="2">
1
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332 <element name="mbr_test1_match">
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333 <assert_contents>
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334 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
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335 <has_text text="NH2-RDVGINNTVK-COOH"/>
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336 </assert_contents>
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337 </element>
0
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338 </output_collection>
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339 </test>
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340 </tests>
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341 <help>
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342 <![CDATA[
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343
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344 **Description**
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345
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346 moFF (a Modest Feature Finder) is an OS independent tool designed to extract
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347 apex MS1 intensity using a set of identified MS2 peptides.
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348 It currently uses a Go library to directly extract data from Thermo Raw spectrum files,
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349 eliminating the need for conversions from other formats.
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350 Moreover, moFF also allows one to work directly with mzML files.
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351
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352 **Usage**
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353
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354 *Modules:*
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355
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356 1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.
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357 2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time.
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358 3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files.
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359
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360 If both match between runs and apex intensity are desired, it is best to run them both at once (i.e., run the 'All' module).
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361 The MBR module is mainly useful for observing the intermediate steps of the algorithm - its outputs are not able to be used as inputs in moFF or in other tools.
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362 If quantification of multiple files without MBR is desired, the apex intensity module may be run with multiple files or a dataset collection in batch mode.
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363 In either case, moFF must be given the paired files at the same time - thus the best method is to construct a dataset collection in which the raw and identification files are in the same order.
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364
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365 *Inputs:*
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366
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367 - Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker.
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368 If it is a generic tabular file, please select the columns corresponding to the required information.
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369 - MS/MS file: this can either be a Thermo raw file or an mzML file.
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370
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371 A given pair of files must have the *exact* same display name, not including the extension;
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372 e.g. ``example1.tabular`` and ``example1.mzml``.
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373 If the display names are different, simply change them in the history menu.
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374 For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections.
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375 This allows for usage of the output dataset collections in workflows.
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376
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377 *Parameters:*
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378
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379 All the parameters related to the the time windows (``rt_w``, ``rt_p``, ``rt_p_match``) are basically the
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380 half of the entire time windows where the apex peak is searched or the XIC is retrieved.
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381 For correct rt windows, we suggest you set the ``rt_p`` value equal to or slighly greater than the
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382 dynamic exclusion duration set in your machine. We suggest also to set the
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383 ``rt_p_match`` always slightly bigger than tha values used for ``rt_p``.
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384 *Outputs:*
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385 When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file,
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386 and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"),
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387 the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary.
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388 If used with a generic tabular format, the only columns in the output file are the 7 columns selected while using moFF plus the columns that moFF adds. Other columns are discarded.
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389
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390 **More Information**
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391
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392 See the moFF Github site at https://github.com/compomics/moFF,
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393 and the publication at https://dx.doi.org/10.1038/nmeth.4075
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394 ]]>
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395 </help>
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396 <citations>
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397 <citation type="doi">10.1038/nmeth.4075</citation>
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398 </citations>
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399 </tool>