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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 94f746247c464fb270358421399810d8a9fb9e8a
author computational-metabolomics
date Fri, 13 Sep 2024 13:36:43 +0000
parents 13034c3886f2
children
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a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 <tool id="mspurity_purityx" name="msPurity.purityX" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset.
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3 </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$__tool_directory__/purityX.R'
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10 --xset_path='$xset'
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11 --out_dir='.'
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12 --minOffset=$minoffset
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13 --maxOffset=$maxoffset
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14 --singleFile=$singleFile
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15 --purityType=$purityType
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16 --cores=\${GALAXY_SLOTS:-4}
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17 #if $xgroups.xgroups == "choose"
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18 --xgroups='$xgroups.xgroups_value'
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19 #end if
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20 --camera_xcms=$camera_xcms
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21
0
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22 --iwNorm=$iw_norm
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23 --ilim=$ilim
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24 #if $isotopes.isotopes == "exclude_default"
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25 --exclude_isotopes
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26 #elif $isotopes.isotopes == "user"
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27 --exclude_isotopes
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28 --isotope_matrix='$isotopes.im'
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29 #end if
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30 #if $file_load_conditional.file_load_select == 'yes'
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31 --galaxy_files='
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32 #for $i in $file_load_conditional.input
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33 $i,
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34 #end for
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35 '
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36 #end if
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37 #if $file_load_conditional.file_load_select == 'yes'
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38 --files='
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39 #for $i in $file_load_conditional.input
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40 $i.name,
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41 #end for
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42 '
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43 #end if
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44
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45 #if $choose_class_cond.choose_class== 'choose'
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46 --choose_class=$choose_class_cond.class
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47 #end if
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48 #if $ignore_files_cond.ignore_files_choice== 'choose'
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49 --ignore_files=$ignore_files_cond.ignore_files
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50 #end if
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51
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52 #if $raw_rt_columns
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53 --rtraw_columns
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54 #end if
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55
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56
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57 ]]></command>
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58 <inputs>
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59
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60 <param argument="--xset" type="data" format="rdata"
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61 help="xcmsSet object saved as an RData file"/>
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62 <expand macro="offsets" />
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63 <expand macro="general_params" />
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64 <param argument="--singleFile" type="integer" label="singleFile" value="0"
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65 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
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66 Uses the index of the files in xcmsSet object. If zero this is ignored"/>
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67
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68 <conditional name="choose_class_cond">
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69 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
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70 <option value="choose">Choose class</option>
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71 <option value="all" selected="true">calculate average across all classes</option>
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72 </param>
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73 <when value="all">
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74 </when>
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75 <when value="choose">
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76 <param argument="--class" type="text" label="Choose class"
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77 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
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78 i.e. xset@phenoData). An average will across all the choosen classes." />
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79 </when>
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80 </conditional>
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81
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82 <conditional name="ignore_files_cond">
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83 <param name="ignore_files_choice" type="select" label="Ignore files?" >
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84 <option value="choose">Choose files to ignore from calculation</option>
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85 <option value="none" selected="true" >Include all files of selected classes in calculation</option>
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86 </param>
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87 <when value="none">
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88 </when>
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89 <when value="choose">
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90 <param argument="--ignore_files" type="text" label="ignore files"
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91 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" />
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92 </when>
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93 </conditional>
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94
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95
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96 <conditional name="xgroups">
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97 <param name="xgroups" type="select" label="xgroups" >
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98 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
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99 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
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100 </param>
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101 <when value="choose">
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102 <param name="xgroups_value" type="text" label="xgroup ids"
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103 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
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104 </when>
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105 <when value="all"/>
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106 </conditional>
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107
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108
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109 <param argument="--purityType" type="select" label="Method of averaging purity"
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110 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
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111 <option value="purityFWHMmedian" selected="true" >FWHM median</option>
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112 <option value="purityFWHMmean" >FWHM mean</option>
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113 <option value="purityFWmedian" >FW median</option>
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114 <option value="purityFWmean" >FW mean</option>
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115 </param>
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116
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117 <expand macro="camera_xcms" />
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118
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119 <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
11
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120 help="[Deprecated] No longer applicable. Previously when obiwarp was used
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121 the retention time correction tracking was slightly different to the other correction methods. To ensure
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122 correct tracking with obiwarp an additional tool (track_rt_raw) was performed prior to
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123 any retention time correction - and this was then checked when this flag was turned on"/>
0
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124
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125 <expand macro="fileload" />
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126
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127 </inputs>
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128 <outputs>
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129 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
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130 from_work_dir="purityX_output.tsv" />
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131 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
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132 from_work_dir="purityX_output.RData" />
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133 </outputs>
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134 <tests>
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135 <test>
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136 <conditional name="file_load_conditional">
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137 <param name="file_load_select" value="yes"/>
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138 <param name="input" >
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139 <collection type="list">
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140 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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141 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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142 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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143 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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144 </collection>
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145 </param>
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146 </conditional>
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147 <conditional name="xgroups">
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148 <param name="xgroups" value="choose"/>
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149 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
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150 </conditional>
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151 <param name="iw_norm" value="QE5" />
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152 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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153 <output name="purityX_tsv" value="purityX_output.tsv" />
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154 <output name="purityX_rdata" value="purityX_output.RData" ftype="rdata" compare="sim_size"/>
0
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155 </test>
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156 </tests>
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157 <help><![CDATA[
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158
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159 ===================================================================
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160 Calculate anticipated precursor ion purity from LC-MS XCMS dataset
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161 ===================================================================
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162 -----------
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163 Description
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164 -----------
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165
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166 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
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167 XCMS determined features
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168
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169 --------------
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170 Output example
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171 --------------
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172 Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
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173 metrics regarding the anticipated precursor ion purity.
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174
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175 ============= ============= ============= ================ ================ ================ ================ ================ ================
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176 grpid meanPurity medianPurity sdPurity stdePurity cvPurity pknmPurity i mz
0
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177 ============= ============= ============= ================ ================ ================ ================ ================ ================
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178 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758
0
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179 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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180 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084
0
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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181 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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182 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781
0
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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183 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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184 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914
0
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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185 ============= ============= ============= ================ ================ ================ ================ ================ ================
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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186
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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187
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b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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188 (Note - the additional peakID column is the same as grpid. Included for compatibility with other Galaxy tools)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
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189
0
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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190
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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191 ]]></help>
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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192 <expand macro="citations" />
a141be614e76 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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193 </tool>