Mercurial > repos > lecorguille > xcms_plot_chromatogram

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author lecorguille
date Thu, 08 Mar 2018 02:48:44 -0500
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1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
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2 <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience</description>
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3
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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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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_plot_chromatogram.r
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14 image '$image'
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16 @COMMAND_FILE_LOAD@
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17 ]]></command>
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19 <inputs>
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20 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />
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22 <expand macro="input_file_load"/>
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23 </inputs>
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25 <outputs>
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26 <data name="ticsPdf" format="pdf" label="${image.name[:-6]}.TICs.pdf" from_work_dir="TICs.pdf"/>
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27 <data name="bpisPdf" format="pdf" label="${image.name[:-6]}.BPIs.pdf" from_work_dir="BPIs.pdf" />
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28 </outputs>
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29
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30 <tests>
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31 <test>
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32 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
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33 <expand macro="test_file_load_single"/>
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34 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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35 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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36 </test>
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37 </tests>
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38
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39 <help><![CDATA[
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41 @HELP_AUTHORS@
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42
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43 ======================
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44 xcms plot chromatogram
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45 ======================
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46
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47 -----------
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48 Description
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49 -----------
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50
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51 This tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience
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52
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53
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54 -----------------
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55 Workflow position
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56 -----------------
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57
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58 **Upstream tools**
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59
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60 ========================= ================= =================== ==========
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61 Name output file format parameter
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62 ========================= ================= =================== ==========
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63 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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64 ------------------------- ----------------- ------------------- ----------
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65 xcms.retcor xset.RData rdata.xcms.retcor RData file
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66 ========================= ================= =================== ==========
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67
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68 .. image:: xcms_plot_chromatogram_workflow.png
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69
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70
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71 ------------
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72 Output files
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73 ------------
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74
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75 **Total Ion Current (TIC) chromatogram**
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76 | Sum of intensity (Y) of all ions detected at each retention time(X)
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77
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78 **Base Peak Intensity Chromatogram (BPI)**
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79 | Sum of intensity (Y) of the most intense peaks at each retention time(X)
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80
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81 ---------------------------------------------------
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83 Changelog/News
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84 --------------
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85
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86 **Version 3.0.0.0 - 07/03/2018**
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87
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88 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace the one created by xcmsSet and retcor tools.
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89
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90 ]]></help>
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
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parents:
diff changeset
91
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
92 <expand macro="citation" />
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
93 </tool>