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annotate purityX.xml @ 15:8f4685455caf draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:32:11 +0000
parents 3ca9866b1d85
children
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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 #if $camera_xcms == "camera"
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22 --rdata_name=xa
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23 #else
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24 --rdata_name=xset
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25 #end if
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26 --iwNorm=$iw_norm
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27 --ilim=$ilim
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28 #if $isotopes.isotopes == "exclude_default"
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29 --exclude_isotopes
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30 #elif $isotopes.isotopes == "user"
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31 --exclude_isotopes
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32 --isotope_matrix='$isotopes.im'
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33 #end if
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34 #if $file_load_conditional.file_load_select == 'yes'
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35 --galaxy_files='
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36 #for $i in $file_load_conditional.input
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37 $i,
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38 #end for
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39 '
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40 #end if
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41 #if $file_load_conditional.file_load_select == 'yes'
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42 --files='
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43 #for $i in $file_load_conditional.input
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44 $i.name,
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45 #end for
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46 '
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47 #end if
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48
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49 #if $choose_class_cond.choose_class== 'choose'
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50 --choose_class=$choose_class_cond.class
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51 #end if
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52 #if $ignore_files_cond.ignore_files_choice== 'choose'
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53 --ignore_files=$ignore_files_cond.ignore_files
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54 #end if
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55
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56 #if $raw_rt_columns
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57 --rtraw_columns
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58 #end if
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59
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60
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61 ]]></command>
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62 <inputs>
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63
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64 <param argument="--xset" type="data" format="rdata"
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65 help="xcmsSet object saved as an RData file"/>
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66 <expand macro="offsets" />
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67 <expand macro="general_params" />
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68 <param argument="--singleFile" type="integer" label="singleFile" value="0"
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69 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
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70 Uses the index of the files in xcmsSet object. If zero this is ignored"/>
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71
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72 <conditional name="choose_class_cond">
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73 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
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74 <option value="choose">Choose class</option>
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75 <option value="all" selected="true">calculate average across all classes</option>
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76 </param>
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77 <when value="all">
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78 </when>
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79 <when value="choose">
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80 <param argument="--class" type="text" label="Choose class"
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81 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
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82 i.e. xset@phenoData). An average will across all the choosen classes." />
0
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83 </when>
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84 </conditional>
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85
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86 <conditional name="ignore_files_cond">
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87 <param name="ignore_files_choice" type="select" label="Ignore files?" >
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88 <option value="choose">Choose files to ignore from calculation</option>
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89 <option value="none" selected="true" >Include all files of selected classes in calculation</option>
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90 </param>
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91 <when value="none">
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92 </when>
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93 <when value="choose">
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94 <param argument="--ignore_files" type="text" label="ignore files"
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95 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" />
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96 </when>
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97 </conditional>
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98
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99
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100 <conditional name="xgroups">
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101 <param name="xgroups" type="select" label="xgroups" >
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102 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
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103 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
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104 </param>
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105 <when value="choose">
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106 <param name="xgroups_value" type="text" label="xgroup ids"
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107 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
0
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108 </when>
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109 <when value="all"/>
0
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110 </conditional>
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111
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112
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113 <param argument="--purityType" type="select" label="Method of averaging purity"
0
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114 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
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115 <option value="purityFWHMmedian" selected="true" >FWHM median</option>
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116 <option value="purityFWHMmean" >FWHM mean</option>
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117 <option value="purityFWmedian" >FW median</option>
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118 <option value="purityFWmean" >FW mean</option>
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119 </param>
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120
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121 <expand macro="camera_xcms" />
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122
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123 <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
0
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124 help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
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125 the retention time correction tracking is slightly different to the other correction methods. To ensure
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126 correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
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127 any retention time correction."/>
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128
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129 <expand macro="fileload" />
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130
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131 </inputs>
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132 <outputs>
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133 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
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134 from_work_dir="purityX.tsv" />
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135 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
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136 from_work_dir="purityX.rdata" />
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137 </outputs>
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138 <tests>
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139 <test>
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140 <conditional name="file_load_conditional">
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141 <param name="file_load_select" value="yes"/>
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142 <param name="input" >
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143 <collection type="list">
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144 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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145 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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146 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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147 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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148 </collection>
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149 </param>
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150 </conditional>
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151 <conditional name="xgroups">
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152 <param name="xgroups" value="choose"/>
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153 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
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154 </conditional>
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155 <param name="iw_norm" value="QE5" />
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156 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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157 <output name="purityX_tsv" value="purityX_output.tsv" />
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158 <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/>
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159 </test>
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160 </tests>
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161 <help><![CDATA[
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162
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163 ===================================================================
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164 Calculate anticipated precursor ion purity from LC-MS XCMS dataset
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165 ===================================================================
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166 -----------
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167 Description
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168 -----------
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169
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170 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
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171 XCMS determined features
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172
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173 --------------
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174 Output example
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175 --------------
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176 Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
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177 metrics regarding the anticipated precursor ion purity.
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178
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179 ============= ============= ============= ================ ================ ================ ================ ================ ================
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180 grpid mean median sd stde RSD pknm i mz
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181 ============= ============= ============= ================ ================ ================ ================ ================ ================
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182 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758
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183 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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184 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084
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185 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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186 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781
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187 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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188 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914
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189 ============= ============= ============= ================ ================ ================ ================ ================ ================
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190
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191
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192
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193 ]]></help>
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194 <expand macro="citations" />
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195 </tool>