Mercurial > repos > lecorguille > msnbase_readmsdata

annotate msnbase_readmsdata.xml @ 12:f6b2750ea32e draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
author workflow4metabolomics
date Tue, 07 Jan 2020 04:30:02 -0500
parents 86a20118e743
children 226fb89cacc4
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12
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
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1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.2">
2
c0a66f15261b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bd62e55afae8b1ea7dd39b5579dea6a0e7bc5d61
lecorguille
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2 <description>Imports mass-spectrometry data files</description>
0
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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4 <macros>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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5 <import>macros.xml</import>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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6 <import>macros_msnbase.xml</import>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 </macros>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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9 <expand macro="requirements"/>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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10 <expand macro="stdio"/>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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"
workflow4metabolomics
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16 #if $os.path.islink(str($input))
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
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17 #set $source = $os.readlink(str($input))
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
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18 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
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19 #else
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
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20 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
f6b2750ea32e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
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21 #end if
0
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22 #else
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23 zipfile '$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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31 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,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: no_unzip.zip, zip. See the help section below." />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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33 </inputs>
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728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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35 <outputs>
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36 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" />
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37 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" >
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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38 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
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39 </data>
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40 </outputs>
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42 <tests>
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728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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44 <test>
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45 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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46 <assert_stdout>
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47 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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48 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
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49 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
8
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lecorguille
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50 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
0
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51 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" />
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52 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" />
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53 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" />
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54 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" />
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55 </assert_stdout>
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56 <output name="sampleMetadata" value="sampleMetadata.tsv" />
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57 </test>
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58 <test>
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59 <param name="input" value="ko15.CDF" ftype="netcdf" />
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60 <assert_stdout>
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61 <has_text text="rowNames: ./ko15.CDF" />
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62 <has_text text="ko15.CDF" />
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63 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
8
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64 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
0
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65 <has_text text="./ko15.CDF ko15 ." />
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66 </assert_stdout>
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67 </test>
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68 <!-- DISABLE FOR TRAVIS
6
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69 Useful to generate test-data for the further steps
0
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70 <test>
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71 <param name="input" value="ko16.CDF" ftype="netcdf" />
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72 <assert_stdout>
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73 <has_text text="rowNames: ./ko16.CDF" />
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74 <has_text text="ko16.CDF" />
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75 <has_text text="./ko16.CDF ko16 ." />
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76 </assert_stdout>
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77 </test>
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78 <test>
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79 <param name="input" value="wt15.CDF" ftype="netcdf" />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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80 <assert_stdout>
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81 <has_text text="rowNames: ./wt15.CDF" />
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82 <has_text text="wt15.CDF" />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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83 <has_text text="./wt15.CDF wt15 ." />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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84 </assert_stdout>
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85 </test>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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86 <test>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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87 <param name="input" value="wt16.CDF" ftype="netcdf" />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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88 <assert_stdout>
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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89 <has_text text="rowNames: ./wt16.CDF" />
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90 <has_text text="wt16.CDF" />
728ebc7ae7dd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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91 <has_text text="./wt16.CDF wt16 ." />
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92 </assert_stdout>
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93 </test>
6
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94 -->
0
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95 </tests>
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96
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97 <help><![CDATA[
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98
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99 @HELP_AUTHORS@
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100
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101 ==================
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102 MSnbase readMSData
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103 ==================
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104
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105 -----------
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106 Description
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107 -----------
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108
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109 Reads as set of XML-based mass-spectrometry data files and
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110 generates an MSnExp object. This function uses the functionality
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111 provided by the ‘mzR’ package to access data and meta data in
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112 ‘mzData’, ‘mzXML’ and ‘mzML’.
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113
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114 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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115
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116
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117 -----------------
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118 Workflow position
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119 -----------------
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120
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121 **Upstream tools**
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122
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123 ========================= ==========================================
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124 Name Format
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125 ========================= ==========================================
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126 Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip
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127 ========================= ==========================================
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128
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129 The easier way to process is to create a Dataset Collection of the type List
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130
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131 **Downstream tools**
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132
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133 =========================== ==================== ====================
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134 Name Output file Format
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135 =========================== ==================== ====================
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136 xcms.findChromPeaks ``*``.raw.RData rdata.msnbase.raw
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137 =========================== ==================== ====================
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138
6
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139
0
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140
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141 **Example of a metabolomic workflow**
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142
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143 .. image:: msnbase_readmsdata_workflow.png
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144
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145 ---------------------------------------------------
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146
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147
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148
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149 -----------
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150 Input files
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151 -----------
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152
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153 =========================== ==================================
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154 Parameter : num + label Format
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155 =========================== ==================================
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156 OR : Zip file zip
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157 --------------------------- ----------------------------------
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158 OR : Single file mzXML, mzML, mzData, netCDF
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159 =========================== ==================================
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160
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161 **Choose your inputs**
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162
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163 You have two methods for your inputs:
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164
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165 | 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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166 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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167
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168 Zip file: Steps for creating the zip file
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169 -----------------------------------------
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170
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171 **Step1: Creating your directory and hierarchize the subdirectories**
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172
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173
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174 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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175
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176 .. _7Zip: http://www.7-zip.org/
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177
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178 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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179 arabidopsis/wild/01.raw
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180 arabidopsis/mutant/01.raw
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181
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182 **Step2: Creating a zip file**
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183
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184 Create your zip file (*e.g.* arabidopsis.zip).
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185
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186 **Step 3 : Uploading it to our Galaxy server**
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187
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188 If your zip file is less than 2Gb, you can use the Get Data tool to upload it.
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189
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190 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org.
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191
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192 .. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf
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193
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194 For more information, do not hesitate to send us an email at supportATworkflow4metabolomics.org.
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195
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196 Advices for converting your files into mzXML format (XCMS input)
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197 ----------------------------------------------------------------
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198
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199 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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200
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201 **We recommend you the following parameters:**
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202
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203 Use Filtering: **True**
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204
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205 Use Peak Picking: **True**
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206
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207 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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208
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209 Use zlib: **64**
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210
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211 Binary Encoding: **64**
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213 m/z Encoding: **64**
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215 Intensity Encoding: **64**
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216
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217
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218 ------------
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219 Output files
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220 ------------
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221
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222 xset.RData: rdata.msnbase.raw format
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223
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224 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks".
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225
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226 sampleMetadata.tsv (only when a zip is used)
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227
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228 | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
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229 | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
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230 | 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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231
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232 ---------------------------------------------------
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233
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234 Changelog/News
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235 --------------
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236
8
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237 .. _News: https://bioconductor.org/packages/release/bioc/news/MSnbase/NEWS
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238
11
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239 **Version 2.8.2.1 - 30/04/2019**
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240
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241 - 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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242
8
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243 **Version 2.8.2.0 - 08/04/2019**
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244
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245 - 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.
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246
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247 **Version 2.4.0.0 - 29/03/2018**
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248
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249 - 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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250
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251 ]]></help>
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252
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253 <expand macro="citation" />
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254 </tool>