Mercurial > repos > lecorguille > xcms_fillpeaks

annotate abims_xcms_fillPeaks.xml @ 18:27fbe73c4279 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Mon, 11 Feb 2019 06:11:33 -0500
parents b6b62413936f
children fbcf5f621aa7
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1 <tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.0">
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3 <description>Integrate areas of missing peaks</description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 <import>macros_xcms.xml</import>
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8 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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13 <command><![CDATA[
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14 @COMMAND_RSCRIPT@/xcms_fillpeaks.r
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16 image '$image'
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18 ## Advanced
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19 expandMz $Adv.expandMz
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20 expandRt $Adv.expandRt
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21 ppm $Adv.ppm
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23 @COMMAND_PEAKLIST@
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25 @COMMAND_FILE_LOAD@
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27 @COMMAND_LOG_EXIT@
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29 ]]></command>
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31 <inputs>
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32 <param name="image" type="data" format="rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from groupChromPeaks" />
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34 <section name="Adv" title="Advanced Options" expanded="False">
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35 <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." />
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36 <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/>
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37 <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." />
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38 </section>
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39
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40 <expand macro="input_peaklist_section"/>
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42 <expand macro="input_file_load"/>
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43
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44 </inputs>
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45
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46 <outputs>
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47 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillChromPeaks.RData" from_work_dir="fillpeaks.RData" />
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48 <expand macro="output_peaklist" function="fillpeaks" />
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49 </outputs>
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50
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51 <tests>
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52 <!--<test>
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53 <param name="image" value="xset.group.retcor.group.RData" ftype="rdata"/>
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54 <param name="method" value="chrom"/>
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55 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
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56 <assert_stdout>
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57 <has_text text="object with 4 samples" />
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58 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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59 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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60 <has_text text="Peaks: 199718 (about 49930 per sample)" />
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61 <has_text text="Peak Groups: 48958" />
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62 <has_text text="Sample classes: bio, blank" />
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63 </assert_stdout>
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64 </test>-->
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65 <!-- Issue with fillpeaks because it seems that there are too many NA
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66 <test>
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67 <param name="image" value="faahKO.xset.group.retcor.group.RData" ftype="rdata"/>
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68 <param name="method" value="chrom"/>
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69 <conditional name="peaklist">
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70 <param name="peaklistBool" value="true" />
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71 <param name="convertRTMinute" value="false" />
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72 <param name="numDigitsMZ" value="4" />
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73 <param name="numDigitsRT" value="1" />
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74 </conditional>
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75 <expand macro="test_file_load_zip"/>
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76 <assert_stdout>
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77 <has_text text="object with 4 samples" />
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78 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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79 <has_text text="Mass range: 200.1-600 m/z" />
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80 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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81 <has_text text="Peak Groups: 8209" />
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82 <has_text text="Sample classes: KO, WT" />
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83 </assert_stdout>
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84 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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85 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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86 </test>
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87 <test>
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88 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData" ftype="rdata"/>
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89 <param name="method" value="chrom"/>
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90 <conditional name="peaklist">
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91 <param name="peaklistBool" value="true" />
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92 <param name="convertRTMinute" value="false" />
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93 <param name="numDigitsMZ" value="4" />
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94 <param name="numDigitsRT" value="1" />
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95 </conditional>
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96 <expand macro="test_file_load_single"/>
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97 <assert_stdout>
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98 <has_text text="object with 4 samples" />
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99 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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100 <has_text text="Mass range: 200.1-600 m/z" />
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101 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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102 <has_text text="Peak Groups: 8209" />
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103 <has_text text="Sample classes: KO, WT" />
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104 </assert_stdout>
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105 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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106 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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107 </test>-->
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108 <!--<test>
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109 <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
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110 <conditional name="peaklist">
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111 <param name="peaklistBool" value="true" />
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112 <param name="convertRTMinute" value="false" />
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113 <param name="numDigitsMZ" value="4" />
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114 <param name="numDigitsRT" value="1" />
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115 <param name="naTOzero" value="false" />
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116 </conditional>
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117 <expand macro="test_file_load_single"/>
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118 <assert_stdout>
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119 <has_text text="expandMz: 0" />
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120 <has_text text="expandRt: 0" />
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121 <has_text text="object with 4 samples" />
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122 <has_text text="Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)" />
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123 <has_text text="Mass range: 200.1-600 m/z" />
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124 <has_text text="Peaks: 15230 (about 3808 per sample)" />
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125 <has_text text="Peak Groups: 6332" />
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126 <has_text text="Sample classes: KO, WT" />
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127 </assert_stdout>
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128 <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
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129 <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" />
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130 </test>-->
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131 <test>
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132 <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
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133 <section name="peaklist">
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134 <param name="peaklistBool" value="true" />
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135 <param name="convertRTMinute" value="false" />
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136 <param name="numDigitsMZ" value="4" />
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137 <param name="numDigitsRT" value="1" />
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138 </section>
13
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139 <expand macro="test_file_load_single"/>
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140 <assert_stdout>
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141 <has_text text="expandMz: 0" />
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142 <has_text text="expandRt: 0" />
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143 <has_text text="object with 4 samples" />
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144 <has_text text="Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)" />
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145 <has_text text="Mass range: 200.1-600 m/z" />
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146 <has_text text="Peaks: 15218 (about 3804 per sample)" />
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147 <has_text text="Peak Groups: 6332" />
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148 <has_text text="Sample classes: KO, WT" />
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149 </assert_stdout>
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150 <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
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151 <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.NAless.tsv" />
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152 </test>
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153 </tests>
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154
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155 <help><![CDATA[
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156
4
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157 @HELP_AUTHORS@
0
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158
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159 ===================
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160 xcms fillChromPeaks
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161 ===================
0
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162
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163 -----------
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164 Description
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165 -----------
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166
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167 **Integrate areas of missing peaks**
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168 For each sample, identify peak groups where that sample is not
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169 represented. For each of those peak groups, integrate the signal
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170 in the region of that peak group and create a new peak.
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171
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172
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173
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174 -----------------
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175 Workflow position
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176 -----------------
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177
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178
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179 **Upstream tools**
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180
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181 ========================= ============================ ==================
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182 Name Output file Format
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183 ========================= ============================ ==================
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184 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
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185 ========================= ============================ ==================
0
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186
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187
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188 **Downstream tools**
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189
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190 =========================== =========================== =======================
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191 Name Output file Format
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192 =========================== =========================== =======================
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193 CAMERA.annotate ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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194 --------------------------- --------------------------- -----------------------
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195 xcms.process_history ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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196 =========================== =========================== =======================
0
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197
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198
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199 **General schema of the metabolomic workflow**
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200
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201 .. image:: xcms_fillpeaks_workflow.png
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202
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203 ---------------------------------------------------
0
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204
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205 ----------
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206 Parameters
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207 ----------
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208
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209 | See the fillChromPeaks_manual_
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210
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211 .. _fillChromPeaks_manual: https://rdrr.io/bioc/xcms/man/fillChromPeaks.html
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212
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213 @HELP_XCMS_MANUAL@
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214
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215 @HELP_PEAKLIST@
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216
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217 ------------
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218 Output files
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219 ------------
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220
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221 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
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222
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223 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.process_history** step of the workflow.
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224
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225 @HELP_PEAKLIST_OUTPUT@
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226
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227
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228 ---------------------------------------------------
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229
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230 Changelog/News
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231 --------------
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232
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233 **Version 3.4.3.0 - 08/02/2019**
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234
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235 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3
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236
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237 - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378
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238
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239
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240 **Version 3.0.0.2 - 09/11/2018**
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241
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242 - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
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243
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244
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245 **Version 3.0.0.1 - 09/10/2018**
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246
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247 - IMPROVEMENT: the export of the PeakList is now mandatory
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248
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249
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250 **Version 3.0.0.0 - 08/03/2018**
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251
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252 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
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253
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254 - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks
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255
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256 - UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm
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257
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258
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259 **Version 2.1.1 - 29/11/2017**
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260
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261 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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262
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263
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264 **Version 2.1.0 - 07/02/2017**
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265
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266 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
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267
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268 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
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269
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270
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271 **Version 2.0.8 - 22/12/2016**
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273 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
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274
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275
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276 **Version 2.0.7 - 06/07/2016**
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278 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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279
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280
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281 **Version 2.0.6 - 04/04/2016**
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282
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283 - TEST: refactoring to pass planemo test using conda dependencies
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284
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285
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286 **Version 2.0.5 - 10/02/2016**
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287
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288 - BUGFIX: better management of errors. Datasets remained green although the process failed
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289
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290 - UPDATE: refactoring of internal management of inputs/outputs
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291
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292 - UPDATE: refactoring to feed the new report tool
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293
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294
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295 **Version 2.0.2 - 02/06/2015**
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296
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297 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
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298
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299 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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300
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301
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302 ]]></help>
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303
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305 <expand macro="citation" />
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308 </tool>