annotate msnbase_readmsdata.xml @ 17:6de175c1f6ef draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 16:03:15 +0000
parents 12def6edac2f
children
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12def6edac2f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 03db090375a4ceb553dbf5ae77ef3866e98fbe9e
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1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy2">
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2 <description>Imports mass-spectrometry data files</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_msnbase.xml</import>
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7 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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12 <command><![CDATA[
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 @COMMAND_RSCRIPT@/msnbase_readmsdata.r
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728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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15 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
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f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
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16 #if $os.path.islink(str($input))
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
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17 #set $source = $os.readlink(str($input))
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18 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'
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19 #else
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20 singlefile_galaxyPath '$input' singlefile_sampleName '$input.element_identifier'
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21 #end if
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22 #else
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23 zipfile '$input'
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24 #end if
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728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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26 @COMMAND_LOG_EXIT@
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27 ]]></command>
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29 <inputs>
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30
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31 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: zip. See the help section below." />
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33 </inputs>
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34
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35 <outputs>
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36 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" />
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37 </outputs>
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39 <tests>
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40
16
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41 <test expect_num_outputs="1">
0
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42 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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43 <assert_stdout>
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44 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
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45 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
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46 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
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47 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (33 total)" />
0
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48 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" />
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49 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" />
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50 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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51 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" />
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52 </assert_stdout>
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53 </test>
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54 <test expect_num_outputs="1">
0
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55 <param name="input" value="ko15.CDF" ftype="netcdf" />
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56 <assert_stdout>
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57 <has_text text="rowNames: ko15.CDF" />
0
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58 <has_text text="ko15.CDF" />
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59 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
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60 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (33 total)" />
13
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61 <has_text text="ko15.CDF ko15 ." />
0
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62 </assert_stdout>
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63 </test>
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64 <!-- DISABLE FOR TRAVIS
6
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65 Useful to generate test-data for the further steps
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66 <test>
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67 <param name="input" value="ko16.CDF" ftype="netcdf" />
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68 <assert_stdout>
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69 <has_text text="rowNames: ./ko16.CDF" />
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70 <has_text text="ko16.CDF" />
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71 <has_text text="./ko16.CDF ko16 ." />
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72 </assert_stdout>
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73 </test>
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74 <test>
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75 <param name="input" value="wt15.CDF" ftype="netcdf" />
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76 <assert_stdout>
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77 <has_text text="rowNames: ./wt15.CDF" />
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78 <has_text text="wt15.CDF" />
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79 <has_text text="./wt15.CDF wt15 ." />
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80 </assert_stdout>
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81 </test>
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82 <test>
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83 <param name="input" value="wt16.CDF" ftype="netcdf" />
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84 <assert_stdout>
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85 <has_text text="rowNames: ./wt16.CDF" />
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86 <has_text text="wt16.CDF" />
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87 <has_text text="./wt16.CDF wt16 ." />
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88 </assert_stdout>
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89 </test>
6
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90 -->
0
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91 </tests>
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92
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93 <help><![CDATA[
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94
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95 @HELP_AUTHORS@
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96
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97 ==================
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98 MSnbase readMSData
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99 ==================
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100
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101 -----------
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102 Description
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103 -----------
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104
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105 Reads as set of XML-based mass-spectrometry data files and
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106 generates an MSnExp object. This function uses the functionality
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107 provided by the ‘mzR’ package to access data and meta data in
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108 ‘mzData’, ‘mzXML’ and ‘mzML’.
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109
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110 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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111
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112
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113 -----------------
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114 Workflow position
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115 -----------------
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116
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117 **Upstream tools**
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118
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119 ========================= ==========================================
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120 Name Format
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121 ========================= ==========================================
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122 Upload File mzxml,mzml,mzdata,netcdf,zip
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123 ========================= ==========================================
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124
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125 The easier way to process is to create a Dataset Collection of the type List
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126
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127 **Downstream tools**
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128
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129 =========================== ==================== ====================
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130 Name Output file Format
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131 =========================== ==================== ====================
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132 xcms.findChromPeaks ``*``.raw.RData rdata.msnbase.raw
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133 =========================== ==================== ====================
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134
6
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135
0
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136
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137 **Example of a metabolomic workflow**
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138
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139 .. image:: msnbase_readmsdata_workflow.png
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140
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141 ---------------------------------------------------
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142
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143
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145 -----------
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146 Input files
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147 -----------
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148
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149 =========================== ==================================
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150 Parameter : num + label Format
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151 =========================== ==================================
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152 OR : Zip file zip
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153 --------------------------- ----------------------------------
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154 OR : Single file mzXML, mzML, mzData, netCDF
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155 =========================== ==================================
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156
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157 **Choose your inputs**
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158
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159 You have two methods for your inputs:
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160
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161 | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks.
0
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162 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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163
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164 Zip file: Steps for creating the zip file
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165 -----------------------------------------
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166
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167 **Step1: Creating your directory and hierarchize the subdirectories**
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168
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169
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170 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip_ software, otherwise your zip will not be well unzipped on the W4M platform (corrupted zip bug).
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172 .. _7Zip: http://www.7-zip.org/
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173
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174 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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175 arabidopsis/wild/01.raw
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176 arabidopsis/mutant/01.raw
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177
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178 **Step2: Creating a zip file**
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179
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180 Create your zip file (*e.g.* arabidopsis.zip).
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181
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182 **Step 3 : Uploading it to our Galaxy server**
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183
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184 Advices for converting your files into mzXML format (XCMS input)
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185 ----------------------------------------------------------------
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186
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187 We recommend you to convert your raw files into **mzXML** in centroid mode (smaller files); this way the files will be compatible with the xmcs centWave algorithm.
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188
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189 **We recommend you the following parameters:**
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190
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191 Use Filtering: **True**
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192
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193 Use Peak Picking: **True**
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195 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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197 Use zlib: **64**
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198
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199 Binary Encoding: **64**
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200
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201 m/z Encoding: **64**
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202
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203 Intensity Encoding: **64**
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204
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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.RData: rdata.msnbase.raw format
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211
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212 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks".
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213
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214 sampleMetadata.tsv (only when a zip is used)
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215
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216 | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
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217 | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
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218 | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step.
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219
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220 ---------------------------------------------------
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221
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222 Changelog/News
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223 --------------
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224
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225 .. _News: https://lgatto.github.io/MSnbase/news/index.html
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226
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227 **Version 2.16.1+galaxy0 - 08/04/2019**
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228
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229 - UPGRADE: upgrade the MSnbase version from 2.8.2 to 2.16.1 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
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230
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231 **Version 2.8.2.1 - 30/04/2019**
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232
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233 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
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234
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235 **Version 2.8.2.0 - 08/04/2019**
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236
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237 - UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
0
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238
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239 **Version 2.4.0.0 - 29/03/2018**
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240
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241 - NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.
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242
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243 ]]></help>
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244
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245 <expand macro="citation" />
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246 </tool>