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annotate rawtools.xml @ 0:51e4aa55ea04 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
author galaxyp
date Fri, 05 Apr 2019 04:16:26 -0400
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51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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1 <tool id="rawtools" name="Raw Tools" version="@RAWTOOLS_VERSION@.@TOOL_SUBVERSION@" profile="16.04">
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2 <description>
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3 Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files.
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4 </description>
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5 <macros>
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6 <token name="@RAWTOOLS_VERSION@">1.4.2</token>
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7 <token name="@TOOL_SUBVERSION@">0</token>
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8 <xml name="input_fasta">
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9 <param format="fasta" name="input_database" type="data" label="Protein Database"
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10 help="Select FASTA database from history"/>
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11 </xml>
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12 </macros>
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13 <requirements>
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14 <requirement type="package" version="@RAWTOOLS_VERSION@">rawtools</requirement>
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15 </requirements>
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16 <command detect_errors="exit_code">
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17 <![CDATA[
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18 #from datetime import datetime
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19 #import json
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20 #import os
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21 #import re
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22 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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23 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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24 #set $temp_stderr = "rawtools_stderr"
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25 #set $bin_dir = "bin"
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26
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27 mkdir output &&
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28 cwd=`pwd` &&
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29 ## TODO: To remove this patch when dropping support for Galaxy 17_09, adding profile="18.01" to the tool.
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30 export HOME=\$cwd &&
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32 mkdir raws_folder &&
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33 #for $input_raw in $input_raws:
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34 #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw")
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35 ln -s -f '${input_raw}' './raws_folder/${input_name}' &&
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36 #end for
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37
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38 #####################
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39 ## Raw Tools ##
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40 #####################
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41 (rawtools.sh
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43 ## PARSING AND QUANTIFICATION OPTIONS
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44
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45 ## If any processing option is enabled in parsing & quantification, "parse" command is mandatory
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46 #if $pq_options.pq_conditional.matrix_select == "yes" or $pq_options.chromatogram_conditional.chromatogram_select == "yes" or $pq_options.mgf_conditional.mgf_select == "yes" or $pq_options.metrics_boolean == "yes":
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47 parse
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48 #end if
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49 --directory ./raws_folder
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50
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51 ## Generates Matrix file
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52 #if $pq_options.pq_conditional.matrix_select == "yes":
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53 --parse
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54 #end if
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55
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56 ## Generates quantification information
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57 #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.q_conditional.q_select == "yes" :
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58 --quant
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59 --labelingreagent ${pq_options.pq_conditional.q_conditional.q_labeling_reagent}
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60 #end if
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61
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62 ## Unlabeled quant
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63 #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.unlabeledquant_boolean == "yes":
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64 --unlabeledquant
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65 #end if
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66
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67 ## Generates Mgf file
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68 #if $pq_options.mgf_conditional.mgf_select == "yes":
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69 --writemgf
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70 --masscutoff ${pq_options.mgf_conditional.mgf_masscutoff}
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71 ## DEPRECATED --intensitycutoff ${pq_options.mgf_conditional.mgf_intensitycutoff}
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72 #if $pq_options.mgf_conditional.mgf_refinement == "yes":
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73 -R
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74 #end if
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75 #end if
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77 ## Generates chromatogram file
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78 #if $pq_options.chromatogram_conditional.chromatogram_select == "yes":
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79 --chro ${pq_options.chromatogram_conditional.chromatogram_type}${pq_options.chromatogram_conditional.chromatogram_order}
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80 #end if
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81
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82 ## Generates metrics file
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83 #if $pq_options.metrics_boolean == "yes":
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84 --metrics
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85 #end if
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86
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87 --out \$cwd/output
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88
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diff changeset
89 2>> $temp_stderr) &&
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90
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91 cat $temp_stderr 2>&1;
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92 ]]>
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93 </command>
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94 <inputs>
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95 <param format="thermo.raw" name="input_raws" type="data" label="Raw file" multiple="true"
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96 help="Select the raw file from history"/>
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97 <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses a proprietary vendor library; to run it you must agree to the vendor license. Read it at https://github.com/kevinkovalchik/RawTools/blob/master/RawFileReaderLicense">
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98 <validator type="expression" message="You must agree to the vendor license to run RawTools.">True == value</validator>
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99 </param>
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100 <section name="pq_options" expanded="true" title="Parsing and Quantification">
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101 <conditional name="pq_conditional">
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102 <param name="matrix_select" type="select"
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103 label="Create Matrix file"
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104 help="Parses raw file meta and scan data and creates a tab-delimited text file.">
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105 <option value="yes" selected="True">Yes</option>
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106 <option value="no" >No</option>
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107 </param>
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108 <when value="yes">
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109 <conditional name="q_conditional">
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110 <param name="q_select" type="select"
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111 label="Quantification"
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112 help="Also quantifies reporter ions and write results to output matrix.">
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113 <option value="yes" >Yes</option>
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114 <option value="no" selected="True">No</option>
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115 </param>
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116 <when value="yes">
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117 <param name="q_labeling_reagent" label="Labeling reagent" type="select"
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118 help="Reagents used to label peptides.">
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119 <option value="TMT0" selected="True">TMT0</option>
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120 <option value="TMT2" >TMT2</option>
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121 <option value="TMT6" >TMT6</option>
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122 <option value="TMT10" >TMT10</option>
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123 <option value="TMT11" >TMT11</option>
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124 <option value="iTRAQ4" >iTRAQ4</option>
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125 <option value="iTRAQ8" >iTRAQ8</option>
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126 </param>
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127 </when>
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128 <when value="no" />
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129 </conditional>
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130 <param name="unlabeledquant_boolean" label="Unlabeled quant" type="boolean" truevalue="yes" falsevalue="no"
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131 help="Calculate areas of precursor peaks and writes them to the matrix file as ParentPeakArea column."/>
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132 </when>
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133 <when value="no" />
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134 </conditional>
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135
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136 <conditional name="mgf_conditional">
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137 <param name="mgf_select" type="select" label="Creates a mgf file"
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138 help="Creates a standard MGF file.">
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139 <option value="yes" >Yes</option>
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140 <option value="no" selected="True">No</option>
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141 </param>
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142 <when value="yes">
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143 <param name="mgf_masscutoff" label="Mass cutoff" value="0" type="float"
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144 help="Specify a mass cutoff to be applied when generating MGF files. May be of use if removal of reporter ions is desired prior to searching of MS2 spectra."/>
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145 <!--<param name="mgf_intensitycutoff" label="Intensity cutoff" value="0" type="float"
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146 help="Relative intensity cutoff for ions included in a MGF file. The value is relative to the highest intensity ion found in a given scan."/>
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147 -->
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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148 <param name="mgf_refinement" label="Precursor mass and charge refinement" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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149 help="Refine precursor charge and monoisotopic mass assignments. Highly recommended if monoisotopic precursor selection was turned off in the instrument method (or peptide match on a QE instrument)."/>
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150
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151 </when>
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152 <when value="no" />
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153 </conditional>
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154 <conditional name="chromatogram_conditional">
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155 <param name="chromatogram_select" type="select"
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156 label="Create chromatogram"
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157 help="Creates a text file of chromatographic data for investigation or plotting.">
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158 <option value="yes" >Yes</option>
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159 <option value="no" selected="True">No</option>
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160 </param>
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161 <when value="yes">
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162 <param name="chromatogram_type" label="Chromatogram type" type="select" help="MS Level">
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163 <option value="1" selected="True">MS1</option>
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164 <option value="2" >MS2</option>
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165 <option value="3" >MS3</option>
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166 </param>
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167 <param name="chromatogram_order" label="Chromatogram order" type="select" help="MS Order">
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168 <option value="T" >TIC</option>
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169 <option value="B" >Base peak</option>
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170 <option value="TB" selected="True">TIC and base peak</option>
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171 </param>
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172 </when>
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173 <when value="no" />
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174 </conditional>
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175 <param name="metrics_boolean" label="Create metrics" type="boolean" truevalue="yes" falsevalue="no"
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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176 help="Creates a text file containing general metrics about the Ms run." />
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177
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178 </section>
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179
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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180 <!-- TODO: QUALITY CONTROL
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181 <section name="quality_control_options" expanded="false" title="Quality control">
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182
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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183 </section>
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184 -->
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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185
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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186 </inputs>
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187 <outputs>
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188 <!-- Matrix -->
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189
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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190 <collection name="output_matrix" type="list" label="${tool.name} - ${on_string}: Matrix">
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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191 <filter>pq_options['pq_conditional']['matrix_select'] == "yes"</filter>
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192 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Matrix.txt" ext="txt" directory="output"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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193 </collection>
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194
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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195 <!-- MGF file -->
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196
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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197 <collection name="output_mgf" type="list" label="${tool.name} - ${on_string}: MGF">
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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198 <filter>pq_options['mgf_conditional']['mgf_select'] == "yes"</filter>
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199 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mgf" ext="mgf" directory="output"/>
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200 </collection>
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201
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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202 <!-- Chromatogram file -->
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203
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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204 <collection name="output_chromatogram" type="list" label="${tool.name} - ${on_string}: Chromatogram" >
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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205 <filter>pq_options['chromatogram_conditional']['chromatogram_select'] == "yes"</filter>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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206 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Ms_BP_chromatogram.txt" ext="txt" directory="output"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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207 </collection>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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208
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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209 <!-- Metrics file -->
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210
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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211 <collection name="output_metrics" type="list" label="${tool.name} - ${on_string}: Metrics" >
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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212 <filter>pq_options['metrics_boolean'] is True</filter>
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213 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Metrics.txt" ext="txt" directory="output"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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214 </collection>
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215 </outputs>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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216 <tests>
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217
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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218 <!-- Test Matrix -->
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219 <test>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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220 <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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221 <param name="license_agreement" value="true" />
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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222 <param name="pq_conditional|matrix_select" value="yes"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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223 <output_collection name="output_matrix" type="list">
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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224 <element name="really_small" file="really_small.raw_Matrix.txt" ftype="txt" compare="sim_size" delta="3000"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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225 </output_collection>
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226 </test>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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227
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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228 <!-- Test mgf conversion -->
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229 <test>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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230 <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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231 <param name="license_agreement" value="true" />
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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232 <param name="pq_conditional|matrix_select" value="no"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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233 <param name="mgf_conditional|mgf_select" value="yes"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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234 <param name="mgf_conditional|mgf_refinement" value="yes"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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235 <output_collection name="output_mgf" type="list">
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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236 <element name="really_small.raw" ftype="mgf">
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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237 <assert_contents>
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238 <has_text text="PEPMASS=675.248779296875"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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239 <has_text text="RTINSECONDS=73.863181104"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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240 <has_text text="SCANS=36"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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241 <has_text text="121.31165 920.2368"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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242 </assert_contents>
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243 </element>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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244 </output_collection>
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245 </test>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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246 <!-- Test chromatogram -->
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247 <test>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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248 <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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249 <param name="license_agreement" value="true" />
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250 <param name="pq_conditional|matrix_select" value="no"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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251 <param name="chromatogram_conditional|chromatogram_select" value="yes"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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252 <output_collection name="output_chromatogram" type="list" >
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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253 <element name="really_small" file="really_small.raw_Ms_BP_chromatogram.txt" ftype="txt" compare="sim_size" delta="3000"/>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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254 </output_collection>
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255 </test>
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256
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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257
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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258 </tests>
51e4aa55ea04 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
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259 <help>
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260 **What it does**
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261
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262 RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis (to be developed in further versions) of Thermo Orbitrap raw mass spectrometer files.
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263
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264 RawTools is written in C# and uses the Thermo RawFileReader library. RawTools is the replacement for RawQuant Python package.
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265
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266 https://github.com/kevinkovalchik/RawTools
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267
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268 **License**
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269
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270 Raw Tools is a free open-source project, following an Apache License 2.0.
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271
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272 RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
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273 Using this software implies the acceptance of RawFileReader license terms.
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274
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275 </help>
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276 <citations>
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277 <citation type="doi">doi:10.1021/acs.jproteome.8b00721</citation>
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278 </citations>
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279 </tool>