Mercurial > repos > tomnl > anticipated_purity_dims

annotate anticipated_purity_dims.xml @ 27:2edcbcd7206f draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 05:59:34 -0400
parents 3e493f2b2929
children
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1 <tool id="anticipated_purity_dims" name="anticipated_purity_dims" version="0.0.15">
0
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2 <description>Calculate the anticipated precursor ion purity from a DIMS 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
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9 <stdio>
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10 <exit_code range="1:" />
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11 </stdio>
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12 <command interpreter="Rscript"><![CDATA[
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13 anticipated_purity_dims.R
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14 #if $mzML_data.format == "mzML_file"
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15 --mzML_file $mzML_data.source
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16 #elif $mzML_data.format == "library"
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17 --mzML_file $__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source
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18 #end if
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19 --peaks_file=$peaks_file
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20 --out_dir=.
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21 --minOffset=$minoffset
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22 --maxOffset=$maxoffset
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23 --ppm=$ppm
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24 --iwNorm=$iw_norm
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25 --ilim=$ilim
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26 #if $sim
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27 --sim
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28 #end if
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29 #if $remove_NAs
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30 --remove_nas
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31 #end if
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32 #if $dimspy_usage.usage == "dimspy"
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33 --dimspy
5
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34 --file_num_dimspy $dimspy_usage.file_num
0
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35 #end if
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36 #if $isotopes.isotopes == "exclude_default":
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37 --exclude_isotopes
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38 #elif $isotopes.isotopes == "user"
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39 --exclude_isotopes
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40 --isotope_matrix = $isotopes.im
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41 #end if
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42 ]]></command>
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43 <inputs>
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44
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45 <param type="data" name="peaks_file" format="tsv, tabular"
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46 help="tsv or tabular file with one column containing the mz values (column header should be either
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47 mz)"/>
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48
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49 <conditional name="mzML_data">
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50 <param name="format" type="select" label="Choose the source for the dataset" >
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51 <option value="mzML_file" selected="true">.mzML files to check purity from</option>
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52 <option value="library">Library directory name (to be used with dimspy workflows) or path to
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53 to an individual .mzML file</option>
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54 </param>
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55 <when value="mzML_file">
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56 <param name="source" type="data" format="mzml" label="Single *.mzML" argument="--mzML_file" >
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57 <validator type="empty_field" />
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58 </param>
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59 </when>
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60 <when value="library">
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61 <param name="source" type="text"
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62 size="40" label="Library directory containing *.mzml files
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63 or path to an individual *.mzML"
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64 argument="--mzML_file">
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65 <validator type="empty_field" />
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66 </param>
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67 </when>
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68 </conditional>
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69
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70 <expand macro="offsets" />
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71 <expand macro="general_params" />
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72
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73
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74 <param name="ppm" type="float" label="ppm" value="10"
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75 help="ppm tolerance to compare between mz values"/>
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76
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77 <param name="minoffset" type="float" label="minoffset" value="0.5"
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78 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
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79 100.0 then the range would be from 999.5 to 100.0"/>
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80
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81 <param name="remove_NAs" type="boolean" label="Remove rows where mz value is NA or NaN?" help=""/>
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82
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83 <param name="sim" type="boolean" label="SIM-Stitch experiment?" help=""/>
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84
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85 <conditional name="dimspy_usage">
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86 <param name="usage" type="select" label="dimspy peak matrix text file usage?">
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87 <option value="no_dimspy" selected="true">dimspy not used to prepare the mz text file</option>
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88 <option value="dimspy">dimspy used to prepare mz file</option>
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89 </param>
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90 <when value="no_dimspy">
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91 </when>
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92 <when value="dimspy">
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93 <param name="file_num" type="integer" label="File number" value="1"
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94 help="Choose the file number from the dimspy matrix to use to calculate the precursor ion
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95 purity metric (order based on column order). This file will then be looked for in the
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96 library folder to calculate the metric.
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97 "/>
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98 </when>
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99 </conditional>
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100
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101 </inputs>
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102 <outputs>
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103 <data name="anticipated_purity_dims" format="tsv" label="${tool.name} on ${on_string}"
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104 from_work_dir="anticipated_purity_dims.tsv" />
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105 </outputs>
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106 <tests>
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107 <test>
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108 <param name="mzML_data|format" value="mzML_file" />
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109 <param name="mzML_data|source" value="FULL_SCAN.mzML" />
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110 <param name="remove_NAs" value="True" />
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111 <param name="dimspy_usage|usage" value="dimspy" />
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112
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113 <param name="peaks_file" value="dimspy_peakmatrix.tsv" />
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114
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115 <output name="anticipated_purity_dims" value="anticipated_purity_dims.tsv">
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116 </output>
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117 </test>
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118 </tests>
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119
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120
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121
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122 <help><![CDATA[
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123
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124 =============================================================
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125 Calculate anticipated precursor ion purity from DI-MS dataset
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126 =============================================================
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127 -----------
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128 Description
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129 -----------
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130
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131 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior DI-MS dataset. The dataset
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132 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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133 details, function msPurity::dimsPredictPurity()
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134
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135 --------------
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136 Output example
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137 --------------
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138 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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139 mean calculated purity. The standard deviation (sdPurity), coefficient of variation (relative standard deviation)
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140 cvPurity, the standard error of the purity (sdePurity) and the median number of peaks within the isolation window
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141 (medianPeakNum)
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142
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143 ============= ============= ============= ================ ================ ================ ================
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144 mz medianPurity meanPurity sdPurity cvPurity sdePurity medianPeakNum
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145 ============= ============= ============= ================ ================ ================ ================
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146 50.20428 0.39 0.39 0.0007 0.19 0.0005 3
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147 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
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148 56.91206 0.01 0.01 0.0002 4.53 0.0001 12
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149 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
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150 62.02906 0.14 0.13 0.0014 22.63 0.0009 7
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151 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
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152 75.07431 0.93 0.94 0.019 37.87 0.0134 3
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153 ============= ============= ============= ================ ================ ================ ================
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154
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155 ]]></help>
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156 <expand macro="citations" />
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157 </tool>