Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 7:dca722aecb67 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:15:19 -0500
parents 5c7a7484dc51
children 6b5504f877ff
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1 <tool id="xcms_merge" name="xcms findChromPeaks Merger" version="@WRAPPER_VERSION@.0">
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2 <description>Merge xcms findChromPeaks RData in one to be used by group</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 @COMMAND_XCMS_SCRIPT@/xcms_merge.r
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13
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14 images 'c("${"\",\"".join(map(str, $images))}")'
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16 #if str($sampleMetadata) != 'None':
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17 sampleMetadata '$sampleMetadata'
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18 #end if
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19
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20 @COMMAND_FILE_LOAD@
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21 ]]></command>
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23 <inputs>
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24 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="xset RData / xcms.xcmsSet file" help="output file from another xcms.xcmsSet" multiple="true" />
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25 <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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27 <expand macro="input_file_load"/>
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28 </inputs>
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30 <outputs>
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31 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" from_work_dir="merged.RData" />
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32 </outputs>
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34 <tests>
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35 <!--<test>
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36 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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37 <expand macro="test_file_load_single"/>
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38 <assert_stdout>
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39 <has_text text="object with 4 samples" />
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40 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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41 <has_text text="Mass range: 200.1-600 m/z" />
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42 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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43 <has_text text="Peak Groups: 0" />
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44 <has_text text="Sample classes: ." />
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45 </assert_stdout>
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46 </test>-->
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47 <test>
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48 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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49 <expand macro="test_file_load_single"/>
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50 <param name="sampleMetadata" value="sampleMetadata.tab" />
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51 <assert_stdout>
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52 <has_text_matching expression="ko15\s+KO" />
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53 <has_text_matching expression="ko16\s+KO" />
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54 <has_text_matching expression="wt15\s+WT" />
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55 <has_text_matching expression="wt16\s+WT" />
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56 <has_text text="object with 4 samples" />
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57 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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58 <has_text text="Mass range: 200.1-600 m/z" />
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59 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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60 <has_text text="Peak Groups: 0" />
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61 <has_text text="Sample classes: KO, WT" />
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62 </assert_stdout>
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63 </test>
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64 <!--<test expect_failure="True">
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65 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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66 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
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67 <expand macro="test_file_load_single"/>
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68 <assert_stderr>
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69 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
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70 </assert_stderr>
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71 </test>-->
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72 </tests>
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74 <help><![CDATA[
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76 @HELP_AUTHORS@
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77
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78 ==========================
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79 xcms findChromPeaks Merger
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80 ==========================
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82 -----------
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83 Description
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84 -----------
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85
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86 This tool will allow you to run one xcms findChromPeaks process per sample in parallel and then to merge all RData images in one.
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87 The result is then suitable for xcms groupChromPeaks.
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89 You can provide a sampleMetadata table to attribute phenotypic value to your samples.
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92 -----------------
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93 Workflow position
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94 -----------------
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95
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96 **Upstream tools**
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97
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98 ========================= ================= =================== ==========
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99 Name output file format parameter
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100 ========================= ================= =================== ==========
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101 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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102 ------------------------- ----------------- ------------------- ----------
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103 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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104 ------------------------- ----------------- ------------------- ----------
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105 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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106 ------------------------- ----------------- ------------------- ----------
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107 ... ... ... ...
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108 ========================= ================= =================== ==========
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109
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110
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111 **Downstream tools**
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112
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113 +---------------------------+--------------------+-----------------+
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114 | Name | Output file | Format |
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115 +===========================+====================+=================+
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116 |xcms.group | xset.RData | rdata.xcms.raw |
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117 +---------------------------+--------------------+-----------------+
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118
4
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119 .. image:: xcms_merge_workflow.png
0
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120
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121 -----------
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122 Input files
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123 -----------
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124
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125 +---------------------------+-----------------------+
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126 | Parameter : num + label | Format |
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127 +===========================+=======================+
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128 | 1 : RData file | rdata.xcms.raw |
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129 +---------------------------+-----------------------+
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130 | 2 : RData file | rdata.xcms.raw |
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131 +---------------------------+-----------------------+
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132 | N : RData file | rdata.xcms.raw |
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133 +---------------------------+-----------------------+
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134 | Optional : sampleMetadata | tsv or csv |
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135 +---------------------------+-----------------------+
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136
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137 Example of a sampleMetadata:
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138
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139 +---------------------------+------------+
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140 |HU_neg_028 | bio |
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141 +---------------------------+------------+
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142 |HU_neg_034 | bio |
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143 +---------------------------+------------+
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144 |Blanc04 | blank |
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145 +---------------------------+------------+
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146 |Blanc06 | blank |
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147 +---------------------------+------------+
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148 |Blanc09 | blank |
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149 +---------------------------+------------+
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150
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151 ------------
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152 Output files
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153 ------------
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154
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155 xset.merged.RData: rdata.xcms.raw format
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156
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157 | Rdata file that is necessary in the next step of the workflow "xcms.group".
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158
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159 ---------------------------------------------------
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160
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161 Changelog/News
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162 --------------
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163
7
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164 **Version 3.0.0.0 - 14/02/2018**
6
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165
7
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166 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
6
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167
0
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168 **Version 1.0.0 - 03/02/2017**
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169
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170 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
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171
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172 ]]></help>
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173
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174 <expand macro="citation" />
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175 </tool>