Mercurial > repos > lecorguille > xcms_export_samplemetadata
view xcms_export_samplemetadata.xml @ 11:4ea32e46b2d6 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author | workflow4metabolomics |
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date | Mon, 15 Jul 2024 15:57:52 +0000 |
parents | cdab04a1d1d7 |
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<tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <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 =========================== ============ @HELP_XCMS_MANUAL@ --------------------------------------------------- Changelog/News -------------- @HELP_XCMS_NEWVERSION_31200@ @HELP_XCMS_NEWVERSION_3610@ @HELP_XCMS_NEWVERSION_3610@ @HELP_XCMS_NEWVERSION_3440@ **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>