Mercurial > repos > galaxyp > flashlfq

annotate flashlfq.xml @ 15:dd51e0448fdc draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a72ed1b1e61e0f948dc36b220d2746dc6f06bccf"
author galaxyp
date Tue, 07 Apr 2020 07:21:02 +0000
parents fddbd49da3cf
children
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rev   line source
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dd51e0448fdc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a72ed1b1e61e0f948dc36b220d2746dc6f06bccf"
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1 <tool id="flashlfq" name="FlashLFQ" version="1.0.3.1">
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2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.3">flashlfq</requirement>
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5 </requirements>
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dd51e0448fdc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a72ed1b1e61e0f948dc36b220d2746dc6f06bccf"
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6 <stdio>
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7 <regex match="Problem opening .mzML file" level="fatal" source="stdout" description="Proplem opening mzML file." />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #import re
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11 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
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12 ln -s '${idt}' '${idt_path}' &&
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13 mkdir spectrum_dir &&
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14 #for $peak_list in $peak_lists:
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15 #set $ext = '.mzML'
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16 #if $peak_list.extension.endswith('raw')
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17 #set $ext = '.RAW'
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18 #end if
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19 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + $ext
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20 ln -s '${peak_list}' 'spectrum_dir/${input_name}' &&
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21 #end for
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22 #if $experiment.use_design == 'true':
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23 ln -s '${experiment.experimental_design}' 'spectrum_dir/ExperimentalDesign.tsv' &&
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24 #end if
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25 echo 'y' |
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26 FlashLFQ
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27 --idt '$idt_path'
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28 --rep "./spectrum_dir"
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29 --ppm $ppm
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30 --iso $iso
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31 --nis $nis
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32 $int
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33 $chg
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34 $mbr
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35 #if $experiment.use_design == 'true':
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36 $experiment.nor
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37 #if $experiment.bayesian.calculate == 'true':
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38 --bay true
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39 --ctr '$experiment.bayesian.ctr'
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40 #if str($experiment.bayesian.fcc):
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41 --fcc $experiment.bayesian.fcc
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42 #end if
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43 $experiment.bayesian.sha
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44 $experiment.bayesian.rmc
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45 --mcm $experiment.bayesian.mcm
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46 #if str($experiment.bayesian.rns):
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47 --rns $experiment.bayesian.rns
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48 #end if
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49 #end if
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50 #end if
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51 --out out | tee logfile.txt
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52 ]]></command>
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53 <inputs>
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54 <param argument="--idt" type="data" format="tabular" label="identification file"
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55 help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/>
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56 <param name="peak_lists" type="data" format="mzml,raw,thermo.raw" multiple="true" label="spectrum files"/>
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57 <param argument="--ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
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58 <param argument="--iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
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59 <param argument="--nis" type="integer" value="2" min="2" max="30" label="number of isotopes required to be observed"/>
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60 <param argument="--int" type="boolean" truevalue="--int true" falsevalue="" checked="false"
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61 label="integrate peak areas (not recommended)"/>
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62 <param argument="--chg" type="boolean" truevalue="--chg true" falsevalue="" checked="false"
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63 label="use only precursor charge state"/>
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64 <param argument="--mbr" type="boolean" truevalue="--mbr true" falsevalue="" checked="false"
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65 label="match between runs"/>
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66 <param argument="--mrt" type="float" value="2.5" min=".01" max="60" label="maximum MBR window in minutes"/>
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67 <conditional name="experiment">
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68 <param name="use_design" type="select" label="Use experimnetal design for normalization or protein fold-change analysis">
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69 <option value="false">No</option>
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70 <option value="true">Yes</option>
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71 </param>
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72 <when value="false"/>
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73 <when value="true">
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74 <param name="experimental_design" type="data" format="tabular" label="ExperimentalDesign.tsv"/>
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75 <param argument="--nor" type="boolean" truevalue="--nor true" falsevalue="" checked="true"
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76 label="normalize intensity results"/>
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77 <conditional name="bayesian">
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78 <param name="calculate" type="select" label="Perform Bayesian protein fold-change analysis">
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79 <option value="false">No</option>
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80 <option value="true">Yes</option>
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81 </param>
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82 <when value="false"/>
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83 <when value="true">
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84 <param argument="--ctr" type="select" value="" label="control condition for Bayesian protein fold-change analysis">
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85 <options from_dataset="experimental_design">
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86 <column name="name" index="1"/>
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87 <column name="value" index="1"/>
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88 <filter type="static_value" name="heading_ctr" column="1" value="Condition" keep="False"/>
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89 <filter type="unique_value" name="unique_ctr" column="1"/>
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90 <filter type="sort_by" name="sorted_ctr" column="1"/>
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91 </options>
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92 </param>
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93 <param argument="--fcc" type="float" value="" min="0.01" label="fold-change cutoff" optional="true"
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94 help="Leave blank to detemine emperically from data."/>
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95 <param argument="--sha" type="boolean" truevalue="--sha true" falsevalue="" checked="false"
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96 label="use shared peptides for protein quantification"/>
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97 <param argument="--rmc" type="boolean" truevalue="--rmc true" falsevalue="" checked="false"
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98 label="require MS/MS ID in condition"/>
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99 <param argument="--mcm" type="integer" value="500" min="500" label="number of markov-chain monte carlo iterations"/>
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100 <param argument="--rns" type="integer" value="" optional="true" label="random seed"/>
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101 </when>
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102 </conditional>
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103 </when>
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104 </conditional>
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105 </inputs>
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106
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107 <outputs>
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108 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="logfile.txt"/>
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109 <data name="toml" format="txt" label="${tool.name} on ${on_string}: FlashLfqSettings.toml" from_work_dir="out/FlashLfqSettings.toml"/>
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110 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" from_work_dir="out/QuantifiedPeaks.tsv"/>
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111 <data name="quantifiedPeptides" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeptides.tsv" from_work_dir="out/QuantifiedPeptides.tsv"/>
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112 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" from_work_dir="out/QuantifiedProteins.tsv"/>
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113 <data name="foldChange" format="tabular" label="${tool.name} on ${on_string}: BayesianFoldChangeAnalysis.tsv" from_work_dir="out/BayesianFoldChangeAnalysis.tsv">
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114 <filter>'bayesian' in experiment and 'ctr' in experiment['bayesian']</filter>
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115 </data>
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116 </outputs>
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117 <tests>
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118 <test>
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119 <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/>
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120 <param name="peak_lists" value="sliced-mzml.mzML" ftype="mzml"/>
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121 <param name="ppm" value="12"/>
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122 <param name="iso" value="6"/>
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123 <output name="quantifiedPeaks">
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124 <assert_contents>
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125 <has_text text="EGFQVADGPLYR" />
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126 </assert_contents>
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127 </output>
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131 **FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics.
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132 https://github.com/smith-chem-wisc/FlashLFQ/wiki
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133
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134
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135 **Accepted command-line arguments:**
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136
2
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137 ::
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138
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139 --idt [string|identification file path]
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140 --rep [string|directory containing spectral data files]
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141 --out [string|output directory]
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142 --ppm [double|ppm tolerance]
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143 --nor [bool|normalize intensity results]
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144 --mbr [bool|match between runs]
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145 --sha [bool|use shared peptides for protein quantification]
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146 --bay [bool|Bayesian protein fold-change analysis]
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147 --ctr [string|control condition for Bayesian protein fold-change analysis]
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148 --fcc [double|fold-change cutoff for Bayesian protein fold-change analysis]
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149
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150 **Advanced settings:**
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151
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152 ::
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153
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154 --sil [bool|silent mode]
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155 --int [bool|integrate peak areas (not recommended)]
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156 --iso [double|isotopic distribution tolerance in ppm]
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157 --mrt [double|maximum MBR window in minutes]
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158 --chg [bool|use only precursor charge state]
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159 --nis [int|number of isotopes required to be observed]
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160 --rmc [bool|require MS/MS ID in condition]
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161 --mcm [int|number of markov-chain monte carlo iterations for the Bayesian protein fold-change analysis]
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162 --rns [int|random seed for the Bayesian protein fold-change analysis]
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163
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164
3
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165 **Tab-Delimited Identification Text File**
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166
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167 The first line of the text file should contain column headers identifying what each column is. Note that MetaMorpheus (.psmtsv), Morpheus, MaxQuant (msms.txt), and TDPortal tab-delimited column headers are supported natively and such files can be read without modification. For search software that lists decoys and PSMs above 1% FDR (e.g., MetaMorpheus), you may want to remove these prior to FlashLFQ analysis. FlashLFQ will probably crash if ambiguous PSMs are passed into it (e.g., a PSM with more than 2 peptides listed in one line).
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168
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169 The following headers are required in the list of MS/MS identifications:
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170
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171 - **File Name** - File extensions should be tolerated, but no extension is tested more extensively (e.g. use MyFile and not MyFile.mzML)
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172 - **Base Sequence** - Should only contain amino acid sequences, or it will likely result in a crash
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173 - **Full Sequence** - Modified sequence. Can contain any letters, but must be consistent between the same peptidoform to get accurate results
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174 - **Peptide Monoisotopic Mass** - Theoretical monoisotopic mass, including modification mass
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175 - **Scan Retention Time** - MS/MS identification scan retention time
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176 - **Precursor Charge** - Charge of the ion selected for MS/MS resulting in the identification
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177 - **Protein Accession** - Protein accession(s) for the peptide; protein quantification is still preliminary
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178
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179 **ExperimentalDesign File**
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180
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181 The ExperimentalDesign_ File should have 5 columns separated by TAB characters:
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182
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183 - SpectrumFileName - Without the file extension
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184 - Condition - Cannot be blank
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185 - Sample - an integer, at least 1. Each condition must have continuous sample numbers starting at 1. For example, samples 1, 3, and 4 are not valid because sample 2 is missing. In this case you would label the samples as 1, 2, and 3.
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186 - Fraction - an integer, at least 1. Each sample must have continuous fraction numbers starting at 1. If your data is not fractionated, just enter 1 for all fractions. It is OK for two samples to have different total numbers of fractions. It is NOT recommended to use a sample if it is missing a fraction with significant peptide intensity (e.g., if sample 2 is missing fraction #5 out of 10 total fractions).
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187 - Replicate - an integer, at least 1. Each fraction must have continuous replicate numbers starting at 1.
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188
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189 ::
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190
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191 For example, with spectrum files named:
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192
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193 - 20130510_EXQ1_IgPa_QC_UPS1_01.mzml
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194 - 20130510_EXQ1_IgPa_QC_UPS1_02.mzml
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195 - 20130510_EXQ1_IgPa_QC_UPS2_01.mzml
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196 - 20130510_EXQ1_IgPa_QC_UPS2_02.mzml
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197
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198 The ExperimentalDesign File:
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199
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200 FileName Condition Biorep Fraction Techrep
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201 20130510_EXQ1_IgPa_QC_UPS1_01 S1 1 1 1
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202 20130510_EXQ1_IgPa_QC_UPS1_02 S1 2 1 1
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203 20130510_EXQ1_IgPa_QC_UPS2_01 S2 1 1 1
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204 20130510_EXQ1_IgPa_QC_UPS2_02 S2 2 1 1
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205
3
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206
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207 **Outputs**:
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208
9
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209 - **QuantifiedProteins.tsv** - Lists protein accession and in the future will include gene and organism if the TSV contains it. The intensity is either a) the sum of the 3 most intense peptides or b) (Advanced protein quant) a weighted-average of the intensities of the peptides assigned to the protein. The weights are determined by how well the peptide co-varies with the other peptides assigned to that protein.
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210
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211 - **QuantifiedPeaks.tsv** - Each chromatographic peak is shown here, even peaks that were not quantifiable (peak intensity = 0). Details about each peak, such as number of PSMs mapped, start/apex/end retention times, ppm error, etc are contained in this file. A peptide can have multiple peaks over the course of a run (e.g., oxidized peptidoforms elute at different times, etc). Ambiguous peaks are displayed with a | (pipe) delimiter to indicate more than one peptide mapped to that peak.
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212
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213 - **QuantifiedPeptides.tsv** - Peptide intensities are summed by modified sequence; this makes it convenient to compare modified peptidoform intensities across runs.
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214
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215 - **Log.txt** - Log of the FlashLFQ run.
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216
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217
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218 .. _FlashLFQ: https://github.com/smith-chem-wisc/FlashLFQ/wiki
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219 .. _ExperimentalDesign: https://github.com/smith-chem-wisc/FlashLFQ/wiki/Experimental-Design
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220
0
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221 ]]></help>
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222 <citations>
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223 <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
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224 </citations>
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225 </tool>