Mercurial > repos > lecorguille > xcms_export_samplemetadata

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:14:35 +0000
parents 94eb263cfab4
children
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workflow4metabolomics
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1 <tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>which need to be filled with extra information</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_xcms.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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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@/xcms_export_samplemetadata.r
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15 images 'c("${"\",\"".join(map(str, $images))}")'
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16 ]]></command>
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18 <inputs>
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19 <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
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20 </inputs>
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22 <outputs>
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23 <data name="sampleMetadataOutput" format="tabular" label="sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" />
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24 </outputs>
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26 <tests>
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27 <test>
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28 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
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29 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
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30 </test>
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31 </tests>
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33 <help><![CDATA[
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35 @HELP_AUTHORS@
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37 =======================
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38 xcms get sampleMetadata
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39 =======================
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41 -----------
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42 Description
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43 -----------
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45 This tool generates a skeleton of sampleMetadata with perhaps some strange sample names which are definitely compatible with xcms and R
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47 This sampleMetadata file have to be filled with extra information as the class, batch information and maybe conditions
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49 -----------------
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50 Workflow position
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51 -----------------
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53 **Upstream tools**
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55 ========================= ===================== ==============================
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56 Name Output file Format
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57 ========================= ===================== ==============================
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58 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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59 ------------------------- --------------------- ------------------------------
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60 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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61 ------------------------- --------------------- ------------------------------
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62 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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63 ------------------------- --------------------- ------------------------------
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64 ... ... ...
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65 ========================= ===================== ==============================
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68 **Downstream tools**
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70 =========================== ==================== ============================
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71 Name Output file Format
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72 =========================== ==================== ============================
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73 xcms.findChromPeaks Merger sampleMetadata.tsv tabular
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74 =========================== ==================== ============================
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76 .. image:: xcms_merge_workflow.png
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78 -----------
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79 Input files
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80 -----------
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82 =========================== ==================================
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83 Parameter : num + label Format
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84 =========================== ==================================
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85 1 : RData file rdata.xcms.findchrompeaks
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86 --------------------------- ----------------------------------
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87 2 : RData file rdata.xcms.findchrompeaks
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88 --------------------------- ----------------------------------
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89 N : RData file rdata.xcms.findchrompeaks
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90 =========================== ==================================
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95 ------------
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96 Output files
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97 ------------
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99 Example of a sampleMetadata:
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101 =========================== ============
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102 sample_name class
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103 =========================== ============
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104 HU_neg_028 bio
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105 --------------------------- ------------
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106 HU_neg_034 bio
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107 --------------------------- ------------
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108 Blanc04 blank
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109 --------------------------- ------------
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110 Blanc06 blank
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111 --------------------------- ------------
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112 Blanc09 blank
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113 =========================== ============
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114
10
cdab04a1d1d7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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115 @HELP_XCMS_MANUAL@
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116
0
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117 ---------------------------------------------------
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118
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119 Changelog/News
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120 --------------
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121
9
94eb263cfab4 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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122 @HELP_XCMS_NEWVERSION_31200@
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123
94eb263cfab4 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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124 @HELP_XCMS_NEWVERSION_3610@
4
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125
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c684ccd89267 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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126 @HELP_XCMS_NEWVERSION_3610@
c684ccd89267 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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127
c684ccd89267 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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128 @HELP_XCMS_NEWVERSION_3440@
4
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129
0
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130 **Version 3.0.0.0 - 09/10/2018**
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131
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132 - NEW: a new tool to generate a sampleMetadata file you will be able to complete
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133
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134 ]]></help>
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135
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136 <expand macro="citation" />
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137 </tool>