Mercurial > repos > lecorguille > xcms_export_samplemetadata
diff xcms_export_samplemetadata.xml @ 0:e3c06320f884 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
author | lecorguille |
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date | Tue, 09 Oct 2018 12:50:47 -0400 |
parents | |
children | 8c62030a1136 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_export_samplemetadata.xml Tue Oct 09 12:50:47 2018 -0400 @@ -0,0 +1,127 @@ +<tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@WRAPPER_VERSION@.0"> + <description>which need to be filled with extra information</description> + + <macros> + <import>macros.xml</import> + <import>macros_xcms.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + @COMMAND_RSCRIPT@/xcms_export_samplemetadata.r + + images 'c("${"\",\"".join(map(str, $images))}")' + ]]></command> + + <inputs> + <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" /> + </inputs> + + <outputs> + <data name="sampleMetadataOutput" format="tabular" label="sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" /> + </outputs> + + <tests> + <test> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> + <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" /> + </test> + </tests> + + <help><![CDATA[ + +@HELP_AUTHORS@ + +======================= +xcms get sampleMetadata +======================= + +----------- +Description +----------- + +This tool generates a skeleton of sampleMetadata with perhaps some strange sample names which are definitely compatible with xcms and R + +This sampleMetadata file have to be filled with extra information as the class, batch information and maybe conditions + +----------------- +Workflow position +----------------- + +**Upstream tools** + +========================= ===================== ============================== +Name Output file Format +========================= ===================== ============================== +xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------- ------------------------------ +xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------- ------------------------------ +xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------- ------------------------------ +... ... ... +========================= ===================== ============================== + + +**Downstream tools** + +=========================== ==================== ============================ +Name Output file Format +=========================== ==================== ============================ +xcms.findChromPeaks Merger sampleMetadata.tsv tabular +=========================== ==================== ============================ + +.. image:: xcms_merge_workflow.png + +----------- +Input files +----------- + +=========================== ================================== +Parameter : num + label Format +=========================== ================================== +1 : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +2 : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +N : RData file rdata.xcms.findchrompeaks +=========================== ================================== + + + + +------------ +Output files +------------ + +Example of a sampleMetadata: + +=========================== ============ +sample_name class +=========================== ============ +HU_neg_028 bio +--------------------------- ------------ +HU_neg_034 bio +--------------------------- ------------ +Blanc04 blank +--------------------------- ------------ +Blanc06 blank +--------------------------- ------------ +Blanc09 blank +=========================== ============ + +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 3.0.0.0 - 09/10/2018** + +- NEW: a new tool to generate a sampleMetadata file you will be able to complete + + ]]></help> + + <expand macro="citation" /> +</tool>