Mercurial > repos > computational-metabolomics > mspurity_dimspredictpuritysingle

annotate dimsPredictPuritySingle.xml @ 5:067566eef56f draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b1b879e29d5d6c97fdc3636aa6e900ad03695f9e"
author computational-metabolomics
date Fri, 13 Nov 2020 09:45:33 +0000
parents e96082a25ff0
children 2ce66d2f6a24
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1 <tool id="mspurity_dimspredictpuritysingle" name="msPurity.dimsPredictPuritySingle" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>Calculate the anticipated precursor ion purity from a DIMS dataset.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$__tool_directory__/dimsPredictPuritySingle.R'
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9 #if $mzML_data.format == 'mzML_file'
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10 --mzML_file '$mzML_data.source'
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11 #elif $mzML_data.format == 'library'
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12 --mzML_file '$__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source'
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13 #elif $mzML_data.format == 'mzML_data_collection'
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14 --mzML_files='
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15 #for $i in $mzML_data.source
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16 $i,
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17 #end for
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18 '
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19 --galaxy_names='
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20 #for $i in $mzML_data.source
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21 $i.name,
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22 #end for
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23 '
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24 --mzML_filename=' $mzML_data.mzML_filename'
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25
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26 #end if
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27 --peaks_file='$peaks_file'
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28 --out_dir='.'
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29 --minoffset=$minoffset
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30 --maxoffset=$maxoffset
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31 --ppm=$ppm
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32 --iwNorm=$iw_norm
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33 --ilim=$ilim
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34 #if $sim
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35 --sim
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36 #end if
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37 #if $remove_NAs
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38 --remove_nas
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39 #end if
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40 #if $dimspy_usage.usage == "dimspy"
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41 --dimspy
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42 --file_num_dimspy $dimspy_usage.file_num_dimspy
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43 #end if
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44 #if $isotopes.isotopes == "exclude_default":
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45 --exclude_isotopes
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46 #elif $isotopes.isotopes == "user"
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47 --exclude_isotopes
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48 --isotope_matrix = '$isotopes.im'
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49 #end if
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50 ]]></command>
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51 <inputs>
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52
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53 <param argument="--peaks_file" type="data" format="tsv, tabular"
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54 help="tsv or tabular file with one column containing the mz values (column header should be either
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55 mz)"/>
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56
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57 <conditional name="mzML_data">
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58 <param name="format" type="select" label="Choose the source for the dataset" >
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59 <option value="mzML_file" selected="true">A single .mzML files to check purity from</option>
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60 <option value="library">Library directory name (to be used with dimspy workflows) or path to
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61 to an individual .mzML file</option>
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62 <option value="mzML_data_collection" selected="true">A data collection of .mzML files</option>
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63 </param>
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64 <when value="mzML_file">
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65 <param argument="--mzML_file" name="source" type="data" format="mzml" label="Single *.mzML" >
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66 <validator type="empty_field" />
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67 </param>
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68 </when>
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69 <when value="mzML_data_collection">
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70 <param argument="--mzML_files" name="source" type="data_collection"
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71 label="Data collection containing *.mzml files" >
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72 <validator type="empty_field" />
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73 </param>
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74 <param argument="--mzML_filename" type="text" label="Name of file to to calculate purity from" help=""/>
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75 </when>
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76
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77 <when value="library">
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78 <param argument="--mzML_file" name="source" type="text"
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79 size="40" label="Library directory containing *.mzml files (dimspy input only)
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80 or path to an individual .mzML file">
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81 <validator type="empty_field" />
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82 </param>
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83 </when>
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84
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85 </conditional>
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86
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87 <expand macro="general_params" />
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88 <expand macro="offsets" />
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89
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90 <param argument="--ppm" type="float" label="ppm" min="0" value="10"
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91 help="ppm tolerance to compare between mz values"/>
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92 <param argument="--remove_NAs" type="boolean" label="Remove rows where mz value is NA or NaN?" help=""/>
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93 <param argument="--sim" type="boolean" label="SIM-Stitch experiment?" help=""/>
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94 <conditional name="dimspy_usage">
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95 <param name="usage" type="select" label="dimspy peak matrix text file usage?">
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96 <option value="no_dimspy" selected="true">dimspy not used to prepare the mz text file</option>
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97 <option value="dimspy">dimspy used to prepare mz file</option>
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98 </param>
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99 <when value="no_dimspy">
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100 </when>
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101 <when value="dimspy">
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102 <param argument="--file_num_dimspy" type="integer" label="File number" min="0" value="1"
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103 help="Choose the file number from the dimspy matrix to use to calculate the precursor ion
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104 purity metric (order based on column order). This file will then be looked for in the
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105 library folder to calculate the metric.
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106 "/>
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107 </when>
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108 </conditional>
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109
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110 </inputs>
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111 <outputs>
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112 <data name="dimsPredictPuritySingle_output" format="tsv" label="${tool.name} on ${on_string}"
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113 from_work_dir="dimsPredictPuritySingle_output.tsv" />
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114 </outputs>
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115 <tests>
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116 <test>
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117 <param name="mzML_data|format" value="mzML_file" />
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118 <param name="mzML_data|source" value="dimsPredictPuritySingle_full_scan.mzML" />
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119 <param name="remove_NAs" value="True" />
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120 <param name="dimspy_usage|usage" value="dimspy" />
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121 <param name="dimspy_usage|file_num_dimspy" value="1" />
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122 <param name="peaks_file" value="dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv" />
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123 <output name="dimsPredictPuritySingle_output" value="dimsPredictPuritySingle_output.tsv" />
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124 </test>
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125 </tests>
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126
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127
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128
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129 <help><![CDATA[
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130
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131 =============================================================
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132 Calculate anticipated precursor ion purity from DI-MS dataset
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133 =============================================================
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134 -----------
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135 Description
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136 -----------
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137
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138 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior DI-MS dataset. The dataset
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139 can either be in the form of multiple 'full scans' or a SIM-Stitch dataset. See the Bioconductor documentation for more
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140 details, function msPurity::dimsPredictPurity()
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141
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142 --------------
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143 Output example
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144 --------------
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145 Output consists of the mz column (along with any other columns that were in the original mz file). The median and
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146 mean calculated purity. The standard deviation (sdPurity), coefficient of variation (relative standard deviation)
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147 cvPurity, the standard error of the purity (sdePurity) and the median number of peaks within the isolation window
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148 (medianPeakNum)
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149
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150 ============= ============= ============= ================ ================ ================ ================
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151 mz medianPurity meanPurity sdPurity cvPurity sdePurity medianPeakNum
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152 ============= ============= ============= ================ ================ ================ ================
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153 50.20428 0.39 0.39 0.0007 0.19 0.0005 3
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154 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
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155 56.91206 0.01 0.01 0.0002 4.53 0.0001 12
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156 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
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157 62.02906 0.14 0.13 0.0014 22.63 0.0009 7
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158 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
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159 75.07431 0.93 0.94 0.019 37.87 0.0134 3
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160 ============= ============= ============= ================ ================ ================ ================
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161
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162 ]]></help>
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163 <expand macro="citations" />
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164 </tool>