Mercurial > repos > lecorguille > xcms_fillpeaks

annotate abims_xcms_fillPeaks.xml @ 31:8fd5b5afa24d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:17:29 -0500
parents 6b5ed508f81f
children ea611367e1da
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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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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 @COMMAND_XCMS_SCRIPT@/xcms_fillpeaks.r
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15 image '$image'
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17 ## Advanced
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18 expandMz $Adv.expandMz
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19 expandRt $Adv.expandRt
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20 ppm $Adv.ppm
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22 @COMMAND_PEAKLIST@
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24 @COMMAND_FILE_LOAD@
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26 @COMMAND_LOG_EXIT@
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28 ]]></command>
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30 <inputs>
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31 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
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33 <section name="Adv" title="Advanced Options" expanded="False">
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34 <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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35 <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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36 <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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37 </section>
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39 <expand macro="input_peaklist"/>
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40
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41 <expand macro="input_file_load"/>
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42
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43 </inputs>
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44
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45 <outputs>
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46 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" from_work_dir="fillpeaks.RData" />
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47 <expand macro="output_peaklist" function="fillpeaks" />
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48 </outputs>
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49
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50 <tests>
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51 <!--<test>
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52 <param name="image" value="xset.group.retcor.group.RData"/>
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53 <param name="method" value="chrom"/>
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54 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
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55 <assert_stdout>
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56 <has_text text="object with 4 samples" />
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57 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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58 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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59 <has_text text="Peaks: 199718 (about 49930 per sample)" />
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60 <has_text text="Peak Groups: 48958" />
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61 <has_text text="Sample classes: bio, blank" />
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62 </assert_stdout>
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63 </test>-->
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64 <!-- Issue with fillpeaks because it seems that there are too many NA
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65 <test>
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66 <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
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67 <param name="method" value="chrom"/>
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68 <conditional name="peaklist">
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69 <param name="peaklistBool" value="true" />
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70 <param name="convertRTMinute" value="false" />
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71 <param name="numDigitsMZ" value="4" />
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72 <param name="numDigitsRT" value="1" />
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73 </conditional>
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74 <expand macro="test_file_load_zip"/>
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75 <assert_stdout>
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76 <has_text text="object with 4 samples" />
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77 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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78 <has_text text="Mass range: 200.1-600 m/z" />
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79 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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80 <has_text text="Peak Groups: 8209" />
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81 <has_text text="Sample classes: KO, WT" />
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82 </assert_stdout>
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83 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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84 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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85 </test>
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86 <test>
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87 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
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88 <param name="method" value="chrom"/>
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89 <conditional name="peaklist">
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90 <param name="peaklistBool" value="true" />
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91 <param name="convertRTMinute" value="false" />
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92 <param name="numDigitsMZ" value="4" />
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93 <param name="numDigitsRT" value="1" />
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94 </conditional>
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95 <expand macro="test_file_load_single"/>
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96 <assert_stdout>
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97 <has_text text="object with 4 samples" />
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98 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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99 <has_text text="Mass range: 200.1-600 m/z" />
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100 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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101 <has_text text="Peak Groups: 8209" />
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102 <has_text text="Sample classes: KO, WT" />
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103 </assert_stdout>
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104 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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105 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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106 </test>-->
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107 <test>
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108 <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData"/>
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109 <conditional name="peaklist">
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110 <param name="peaklistBool" value="true" />
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111 <param name="convertRTMinute" value="false" />
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112 <param name="numDigitsMZ" value="4" />
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113 <param name="numDigitsRT" value="1" />
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114 </conditional>
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115 <expand macro="test_file_load_single"/>
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116 <assert_stdout>
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117 <has_text text="expandMz: 0" />
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118 <has_text text="expandRt: 0" />
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119 <has_text text="object with 4 samples" />
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120 <has_text text="Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)" />
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121 <has_text text="Mass range: 200.1-600 m/z" />
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122 <has_text text="Peaks: 15230 (about 3808 per sample)" />
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123 <has_text text="Peak Groups: 6332" />
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124 <has_text text="Sample classes: KO, WT" />
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125 </assert_stdout>
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126 <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
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127 <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" />
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128 </test>
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129 </tests>
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130
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131 <help><![CDATA[
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132
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133 @HELP_AUTHORS@
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134
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135 ===================
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136 xcms fillChromPeaks
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137 ===================
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138
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139 -----------
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140 Description
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141 -----------
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142
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143 **Integrate areas of missing peaks**
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144 For each sample, identify peak groups where that sample is not
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145 represented. For each of those peak groups, integrate the signal
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146 in the region of that peak group and create a new peak.
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147
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148
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149
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150 -----------------
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151 Workflow position
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152 -----------------
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153
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154
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155 **Upstream tools**
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156
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157 ========================= ================= ================== ==========
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158 Name output file format parameter
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159 ========================= ================= ================== ==========
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160 xcms.group xset.group.RData rdata.xcms.group RData file
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161 ========================= ================= ================== ==========
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162
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163
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164 **Downstream tools**
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165
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166 +---------------------------+------------------+-----------------------+
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167 | Name | Output file | Format |
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168 +===========================+==================+=======================+
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169 |CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks |
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170 +---------------------------+------------------+-----------------------+
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171 |xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks |
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172 +---------------------------+------------------+-----------------------+
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173
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174 The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.
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175
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176
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177 **General schema of the metabolomic workflow**
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178
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179 .. image:: xcms_fillpeaks_workflow.png
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180
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181
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182
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183 -----------
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184 Input files
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185 -----------
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186
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187 +---------------------------+-----------------------+
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188 | Parameter : num + label | Format |
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189 +===========================+=======================+
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190 | 1 : RData file | rdata.xcms.group |
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191 +---------------------------+-----------------------+
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192
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193
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194 ----------
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195 Parameters
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196 ----------
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197
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198 | See the fillChromPeaks_manual_
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199
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200 .. _fillChromPeaks_manual: https://rdrr.io/bioc/xcms/man/fillChromPeaks.html
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201
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202 @HELP_XCMS_MANUAL@
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203
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204 @HELP_PEAKLIST@
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205
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206 ------------
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207 Output files
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208 ------------
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209
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210 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
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211
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212 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
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213
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214 xset.variableMetadata.tsv : tabular format
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216 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
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217
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218 xset.dataMatrix.tsv : tabular format
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220 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
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221
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222 ------
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224 .. class:: infomark
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225
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226 The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.
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227
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228
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229 ---------------------------------------------------
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230
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231 ---------------
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232 Working example
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233 ---------------
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234
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235 Input files
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236 -----------
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237
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238 | RData file -> **xset.retcor.RData**
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239
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240 Parameters
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241 ----------
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242
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243 | method -> **chrom**
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244 | Get a Peak List -> **false**
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245
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246
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247 Output files
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248 ------------
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249
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250 | **xset.fillPeaks.RData: RData file**
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251
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252
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253 ---------------------------------------------------
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254
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255 Changelog/News
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256 --------------
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257
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258 **Version 3.0.0.0 - 14/02/2018**
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259
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260 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
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261
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262 - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW)
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263
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264 - UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm
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265
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266 **Version 2.1.1 - 29/11/2017**
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267
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268 - 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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269
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270 **Version 2.1.0 - 07/02/2017**
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272 - 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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273
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274 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
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275
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276 **Version 2.0.8 - 22/12/2016**
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278 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
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279
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280 **Version 2.0.7 - 06/07/2016**
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282 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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283
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284 **Version 2.0.6 - 04/04/2016**
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285
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286 - TEST: refactoring to pass planemo test using conda dependencies
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287
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288 **Version 2.0.5 - 10/02/2016**
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289
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290 - BUGFIX: better management of errors. Datasets remained green although the process failed
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291
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292 - UPDATE: refactoring of internal management of inputs/outputs
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293
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294 - UPDATE: refactoring to feed the new report tool
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295
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296
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297 **Version 2.0.2 - 02/06/2015**
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298
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299 - 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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300
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301 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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302
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303
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304 ]]></help>
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307 <expand macro="citation" />
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308
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310 </tool>