Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 17:ae28a753a6f8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:45:41 +0000
parents 58b5a4b6e1da
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="xcms_merge" name="xcms findChromPeaks Merger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Merge xcms findChromPeaks RData into a unique file to be used by group</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
3
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6 <import>macros_xcms.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 <required_files>
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11 <include path="xcms_merge.r" />
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12 <include path="lib.r" />
ae28a753a6f8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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13 </required_files>
0
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14 <expand macro="stdio"/>
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15
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16 <command><![CDATA[
17
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17 @COMMAND_RSCRIPT@xcms_merge.r
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19 images 'c("${"\",\"".join(map(str, $images))}")'
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21 #if str($sampleMetadata) != 'None':
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22 sampleMetadata '$sampleMetadata'
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23 #end if
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25 @COMMAND_FILE_LOAD@
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26 ]]></command>
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27
3
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28 <inputs>
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29 <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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30 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>
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31
3
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32 <expand macro="input_file_load"/>
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33 </inputs>
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34
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35 <outputs>
3
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36 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="xset.merged.RData" from_work_dir="merged.RData" />
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37 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv">
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38 <filter>not sampleMetadata</filter>
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39 </data>
0
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40 </outputs>
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41
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42 <tests>
3
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43 <!-- DISABLE FOR TRAVIS
0
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44 <test>
3
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45 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
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46 <expand macro="test_file_load_single"/>
0
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47 <assert_stdout>
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48 <has_text text="object with 4 samples" />
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49 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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50 <has_text text="Mass range: 200.1-600 m/z" />
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51 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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52 <has_text text="Peak Groups: 0" />
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53 <has_text text="Sample classes: ." />
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54 </assert_stdout>
3
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55 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
0
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56 </test>
3
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57 -->
15
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58 <test expect_num_outputs="1">
3
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59 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
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60 <expand macro="test_file_load_single"/>
0
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61 <param name="sampleMetadata" value="sampleMetadata.tab" />
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62 <assert_stdout>
3
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63 <has_text_matching expression="ko15\s+KO" />
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64 <has_text_matching expression="ko16\s+KO" />
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65 <has_text_matching expression="wt15\s+WT" />
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66 <has_text_matching expression="wt16\s+WT" />
0
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67 <has_text text="object with 4 samples" />
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68 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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69 <has_text text="Mass range: 200.1-600 m/z" />
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70 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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71 <has_text text="Peak Groups: 0" />
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72 <has_text text="Sample classes: KO, WT" />
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73 </assert_stdout>
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74 </test>
3
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75 <!--<test expect_failure="True">
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76 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
2
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77 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
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78 <expand macro="test_file_load_single"/>
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79 <assert_stderr>
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80 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
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81 </assert_stderr>
3
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82 </test>-->
0
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83 </tests>
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84
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85 <help><![CDATA[
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86
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87 @HELP_AUTHORS@
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88
3
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89 ==========================
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90 xcms findChromPeaks Merger
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91 ==========================
0
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92
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93 -----------
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94 Description
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95 -----------
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96
3
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97 This tool allows you to run one xcms findChromPeaks process per sample in parallel and then to merge all RData images into one.
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98 The result is then suitable for xcms groupChromPeaks.
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99
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100 You can provide a sampleMetadata table to attribute phenotypic values to your samples.
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101
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102
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103 -----------------
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104 Workflow position
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105 -----------------
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106
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107 **Upstream tools**
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108
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109 ========================= ===================== ==============================
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110 Name Output file Format
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111 ========================= ===================== ==============================
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112 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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113 ------------------------- --------------------- ------------------------------
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114 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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115 ------------------------- --------------------- ------------------------------
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116 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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117 ------------------------- --------------------- ------------------------------
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118 ... ... ...
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119 ------------------------- --------------------- ------------------------------
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120 Upload file [optional] sampleMetadata tabular
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121 ========================= ===================== ==============================
0
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122
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123
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124 **Downstream tools**
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125
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126 =========================== ==================== ============================
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127 Name Output file Format
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128 =========================== ==================== ============================
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129 xcms.groupChromPeaks xset.merged.RData rdata.xcms.findchrompeaks
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130 =========================== ==================== ============================
0
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131
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132 .. image:: xcms_merge_workflow.png
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133
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134 -----------
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135 Input files
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136 -----------
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137
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138 =========================== ==================================
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139 Parameter : num + label Format
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140 =========================== ==================================
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141 1 : RData file rdata.xcms.findchrompeaks
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142 --------------------------- ----------------------------------
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143 2 : RData file rdata.xcms.findchrompeaks
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144 --------------------------- ----------------------------------
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145 N : RData file rdata.xcms.findchrompeaks
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146 --------------------------- ----------------------------------
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147 Optional : sampleMetadata tsv or csv
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148 =========================== ==================================
0
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149
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150 Example of a sampleMetadata:
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151
3
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152 =========================== ============
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153 Samples class
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154 =========================== ============
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155 HU_neg_028 bio
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156 --------------------------- ------------
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157 HU_neg_034 bio
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158 --------------------------- ------------
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159 Blanc04 blank
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160 --------------------------- ------------
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161 Blanc06 blank
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162 --------------------------- ------------
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163 Blanc09 blank
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164 =========================== ============
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165
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166
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167 ------------
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168 Output files
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169 ------------
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170
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171 xset.merged.RData: rdata.xcms.findchrompeaks format
0
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172
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173 | Rdata file that is necessary in the next step of the workflow "xcms.groupChromPeaks".
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174
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175 @HELP_XCMS_MANUAL@
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176
0
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177 ---------------------------------------------------
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178
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179 Changelog/News
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180 --------------
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181
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5bd125a3f3b0 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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182 @HELP_XCMS_NEWVERSION_31200@
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183
13
39797c768bba "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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184 @HELP_XCMS_NEWVERSION_3610@
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185
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186 @HELP_XCMS_NEWVERSION_3440@
8
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187
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188 **Version 3.0.0.0 - 08/03/2018**
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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189
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 2
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190 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 2
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191
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 2
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192 - IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data.
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 2
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193
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 2
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194 - IMPROVMENT: the tool will now generate a sampleMetadata file if any was provided. It will be useful to add some further information for the normalization and statistics steps.
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 2
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195
2
3a5204f14fff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 0
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196 **Version 1.0.1 - 13/02/2017**
3a5204f14fff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 0
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197
3a5204f14fff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 0
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198 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
3a5204f14fff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 0
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199
0
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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200 **Version 1.0.0 - 03/02/2017**
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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201
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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202 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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203
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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204 ]]></help>
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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205
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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206 <expand macro="citation" />
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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207 </tool>