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annotate purityX.xml @ 0:ddda01fb1503 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:15:53 -0400
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1 <tool id="mspurity_purityx" name="msPurity.purityX" version="0.2.0">
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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
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8 <expand macro="requirements" />
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9
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command interpreter="Rscript"><![CDATA[
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14 purityX.R
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15 --xset_path=$xset
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16 --out_dir=.
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17 --minOffset=$minoffset
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18 --maxOffset=$maxoffset
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19 --singleFile=$singleFile
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20 --purityType=$purityType
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21 --cores=\${GALAXY_SLOTS:-4}
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22 #if $xgroups.xgroups == "choose"
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23 --xgroups=$xgroups.xgroups_value
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24 #end if
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25 --camera_xcms=$camera_xcms
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26 #if $camera_xcms == "camera"
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27 --rdata_name=xa
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28 #else
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29 --rdata_name=xset
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30 #end if
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31 --iwNorm=$iw_norm
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32 --ilim=$ilim
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33 #if $isotopes.isotopes == "exclude_default"
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34 --exclude_isotopes
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35 #elif $isotopes.isotopes == "user"
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36 --exclude_isotopes
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37 --isotope_matrix=$isotopes.im
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38 #end if
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39 #if $file_load_conditional.file_load_select == 'yes'
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40 --galaxy_files='
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41 #for $i in $file_load_conditional.input
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42 $i,
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43 #end for
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44 '
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45 #end if
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46 #if $file_load_conditional.file_load_select == 'yes'
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47 --files='
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48 #for $i in $file_load_conditional.input
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49 $i.name,
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50 #end for
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51 '
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52 #end if
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53
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54 #if $choose_class_cond.choose_class== 'choose'
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55 --choose_class=$choose_class_cond.class
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56 #end if
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57 #if $ignore_files_cond.ignore_files_choice== 'choose'
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58 --ignore_files=$ignore_files_cond.ignore_files
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59 #end if
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60
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61 #if $raw_rt_columns
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62 --rtraw_columns
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63 #end if
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64
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65
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66 ]]></command>
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67 <inputs>
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68
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69 <param type="data" name="xset" format="rdata"
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70 help="xcmsSet object saved as an RData file"/>
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71 <expand macro="offsets" />
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72 <expand macro="general_params" />
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73 <param name="singleFile" type="integer" label="singleFile" value="0"
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74 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
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75 Uses the index of the files in xcmsSet object. If zero this is ignored"/>
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76
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77 <conditional name="choose_class_cond">
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78 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
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79 <option value="choose">Choose class</option>
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80 <option value="all" selected="true">calculate average across all classes</option>
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81 </param>
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82 <when value="all">
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83 </when>
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84 <when value="choose">
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85 <param name="class" type="text" label="Choose class"
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86 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
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87 i.e. xset@phenoData). An average will across all the choosen classes." />
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88 </when>
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89 </conditional>
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90
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91 <conditional name="ignore_files_cond">
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92 <param name="ignore_files_choice" type="select" label="Ignore files?" >
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93 <option value="choose">Choose files to ignore from calculation</option>
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94 <option value="none" selected="true" >Include all files of selected classes in calculation</option>
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95 </param>
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96 <when value="none">
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97 </when>
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98 <when value="choose">
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99 <param name="ignore_files" type="text" label="ignore files"
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100 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" />
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101 </when>
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102 </conditional>
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103
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104
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105 <conditional name="xgroups">
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106 <param name="xgroups" type="select" label="xgroups" >
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107 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
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108 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
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109 </param>
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110 <when value="all">
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111 </when>
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112 <when value="choose">
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113 <param name="xgroups_value" type="text" label="xgroup ids"
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114 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
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115 </when>
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116 </conditional>
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117
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118
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119 <param name="purityType" type="select" label="Method of averaging purity"
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120 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
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121 <option value="purityFWHMmedian" selected="true" >FWHM median</option>
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122 <option value="purityFWHMmean" >FWHM mean</option>
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123 <option value="purityFWmedian" >FW median</option>
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124 <option value="purityFWmean" >FW mean</option>
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125 </param>
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126
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127 <expand macro="camera_xcms" />
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128
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129 <param name="raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
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130 help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
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131 the retention time correction tracking is slightly different to the other correction methods. To ensure
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132 correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
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133 any retention time correction."/>
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134
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135 <expand macro="fileload" />
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136
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137 </inputs>
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138 <outputs>
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139 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
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140 from_work_dir="purityX.tsv" />
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141 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
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142 from_work_dir="purityX.rdata" />
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143 </outputs>
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144 <tests>
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145 <test>
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146 <conditional name="file_load_conditional">
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147 <param name="file_load_select" value="yes"/>
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148 <param name="input" >
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149 <collection type="list">
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150 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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151 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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152 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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153 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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154 </collection>
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155 </param>
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156 </conditional>
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157 <conditional name="xgroups">
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158 <param name="xgroups" value="choose"/>
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159 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
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160 </conditional>
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161 <param name="iw_norm" value="QE5" />
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162 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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163 <output name="purityX_tsv" value="purityX_output.tsv" />
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164 <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/>
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165 </test>
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166 </tests>
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167 <help><![CDATA[
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168
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169 ===================================================================
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170 Calculate anticipated precursor ion purity from LC-MS XCMS dataset
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171 ===================================================================
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172 -----------
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173 Description
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174 -----------
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175
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176 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
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177 XCMS determined features
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178
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179 --------------
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180 Output example
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181 --------------
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182 Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
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183 metrics regarding the anticipated precursor ion purity.
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184
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185 ============= ============= ============= ================ ================ ================ ================ ================ ================
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186 grpid mean median sd stde RSD pknm i mz
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187 ============= ============= ============= ================ ================ ================ ================ ================ ================
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188 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758
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189 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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190 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084
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191 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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192 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781
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193 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
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194 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914
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195 ============= ============= ============= ================ ================ ================ ================ ================ ================
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196
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199 ]]></help>
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200 <expand macro="citations" />
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201 </tool>