Mercurial > repos > lecorguille > xcms_summary
changeset 25:3a53e63555c7 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 392e432529877680e80a7b338e20d69a42e53767
| author | lecorguille |
|---|---|
| date | Mon, 03 Apr 2017 07:53:49 -0400 |
| parents | 5cc59ee748b6 |
| children | e6a6503d7d6d |
| files | abims_xcms_summary.xml macros.xml static/images/xcms_summary_workflow.png test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html xcms_summary.r |
| diffstat | 6 files changed, 29 insertions(+), 7 deletions(-) [+] |
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--- a/abims_xcms_summary.xml Wed Mar 22 16:07:25 2017 -0400 +++ b/abims_xcms_summary.xml Mon Apr 03 07:53:49 2017 -0400 @@ -57,6 +57,28 @@ This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools +----------------- +Workflow position +----------------- + +**Upstream tools** + +========================= ================= ===================== ========== +Name output file format parameter +========================= ================= ===================== ========== +xcms.xcmsSet xset.RData rdata.xcms.raw RData file +------------------------- ----------------- --------------------- ---------- +xcms.group xset.RData rdata.xcms.group RData file +------------------------- ----------------- --------------------- ---------- +xcms.retcor xset.RData rdata.xcms.retcor RData file +------------------------- ----------------- --------------------- ---------- +xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file +------------------------- ----------------- --------------------- ---------- +CAMERA.annotate xset.RData rdata.camera.* RData file +========================= ================= ===================== ========== + + +.. image:: xcms_merge_workflow.png ---------------------------------------------------
--- a/macros.xml Wed Mar 22 16:07:25 2017 -0400 +++ b/macros.xml Mon Apr 03 07:53:49 2017 -0400 @@ -107,11 +107,11 @@ </conditional> </xml> - <xml name="output_peaklist"> - <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv"> + <xml name="output_peaklist" token_function=""> + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv"> <filter>(peaklist['peaklistBool'])</filter> </data> - <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" > + <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" > <filter>(peaklist['peaklistBool'])</filter> </data> </xml>
--- a/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Wed Mar 22 16:07:25 2017 -0400 +++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Mon Apr 03 07:53:49 2017 -0400 @@ -19,7 +19,7 @@ <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr> <tr> <td> ko15 </td> <td> ./ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> ./ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> ./wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> ./wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr> </table> -<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process. +<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. </div> <h2>Function launched:</h2> <div><table>
--- a/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html Wed Mar 22 16:07:25 2017 -0400 +++ b/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html Mon Apr 03 07:53:49 2017 -0400 @@ -19,7 +19,7 @@ <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr> <tr> <td> ko15 </td> <td> faahKO_reduce/KO/ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> faahKO_reduce/KO/ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> faahKO_reduce/WT/wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> faahKO_reduce/WT/wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr> </table> -<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process. +<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. </div> <h2>Function launched:</h2> <div><table>
--- a/xcms_summary.r Wed Mar 22 16:07:25 2017 -0400 +++ b/xcms_summary.r Mon Apr 03 07:53:49 2017 -0400 @@ -93,11 +93,11 @@ } else if (is.null(md5sumList$removalBadCharacters)) { md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>") md5sumHtml = paste("<td>",md5sumList$origin,"</td>") - md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process." + md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process." } else { md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>") - md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>" + md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>" } writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")