Mercurial > repos > lecorguille > xcms_merge
diff xcms_merge.xml @ 11:67ab853b89f3 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
| author | lecorguille |
|---|---|
| date | Tue, 03 Apr 2018 11:38:21 -0400 |
| parents | 47e953d9da82 |
| children | 2c7d3db37974 |
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--- a/xcms_merge.xml Thu Mar 08 05:52:52 2018 -0500 +++ b/xcms_merge.xml Tue Apr 03 11:38:21 2018 -0400 @@ -3,13 +3,14 @@ <macros> <import>macros.xml</import> + <import>macros_xcms.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ - @COMMAND_XCMS_SCRIPT@/xcms_merge.r + @COMMAND_RSCRIPT@/xcms_merge.r images 'c("${"\",\"".join(map(str, $images))}")' @@ -21,14 +22,14 @@ ]]></command> <inputs> - <param name="images" type="data" format="rdata.xcms.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" /> + <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" /> <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"/> <expand macro="input_file_load"/> </inputs> <outputs> - <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" from_work_dir="merged.RData" /> + <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="xset.merged.RData" from_work_dir="merged.RData" /> <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv"> <filter>not sampleMetadata</filter> </data> @@ -37,7 +38,7 @@ <tests> <!-- DISABLE FOR TRAVIS <test> - <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> <expand macro="test_file_load_single"/> <assert_stdout> <has_text text="object with 4 samples" /> @@ -51,7 +52,7 @@ </test> --> <test> - <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> <expand macro="test_file_load_single"/> <param name="sampleMetadata" value="sampleMetadata.tab" /> <assert_stdout> @@ -68,7 +69,7 @@ </assert_stdout> </test> <!--<test expect_failure="True"> - <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> <param name="sampleMetadata" value="sampleMetadata_missing.tab" /> <expand macro="test_file_load_single"/> <assert_stderr> @@ -101,26 +102,26 @@ **Upstream tools** -========================= ================= =================== ========== -Name output file format parameter -========================= ================= =================== ========== -xcms.xcmsSet xset.RData rdata.xcms.raw RData file -------------------------- ----------------- ------------------- ---------- -xcms.xcmsSet xset.RData rdata.xcms.raw RData file -------------------------- ----------------- ------------------- ---------- -xcms.xcmsSet xset.RData rdata.xcms.raw RData file -------------------------- ----------------- ------------------- ---------- -... ... ... ... -========================= ================= =================== ========== +========================= ================= ============================== ========== +Name output file format parameter +========================= ================= ============================== ========== +xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file +------------------------- ----------------- ------------------------------ ---------- +xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file +------------------------- ----------------- ------------------------------ ---------- +xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file +------------------------- ----------------- ------------------------------ ---------- +... ... ... ... +========================= ================= ============================== ========== **Downstream tools** -+---------------------------+--------------------+-----------------+ -| Name | Output file | Format | -+===========================+====================+=================+ -|xcms.group | xset.RData | rdata.xcms.raw | -+---------------------------+--------------------+-----------------+ +=========================== ==================== ============================ +Name Output file Format +=========================== ==================== ============================ +xcms.group xset.RData rdata.xcms.findchrompeaks +=========================== ==================== ============================ .. image:: xcms_merge_workflow.png @@ -128,37 +129,37 @@ Input files ----------- -+---------------------------+-----------------------+ -| Parameter : num + label | Format | -+===========================+=======================+ -| 1 : RData file | rdata.xcms.raw | -+---------------------------+-----------------------+ -| 2 : RData file | rdata.xcms.raw | -+---------------------------+-----------------------+ -| N : RData file | rdata.xcms.raw | -+---------------------------+-----------------------+ -| Optional : sampleMetadata | tsv or csv | -+---------------------------+-----------------------+ +=========================== ================================== +Parameter : num + label Format +=========================== ================================== +1 : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +2 : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +N : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +Optional : sampleMetadata tsv or csv +=========================== ================================== Example of a sampleMetadata: -+---------------------------+------------+ -|HU_neg_028 | bio | -+---------------------------+------------+ -|HU_neg_034 | bio | -+---------------------------+------------+ -|Blanc04 | blank | -+---------------------------+------------+ -|Blanc06 | blank | -+---------------------------+------------+ -|Blanc09 | blank | -+---------------------------+------------+ +--------------------------- ------------ +HU_neg_028 bio +--------------------------- ------------ +HU_neg_034 bio +--------------------------- ------------ +Blanc04 blank +--------------------------- ------------ +Blanc06 blank +--------------------------- ------------ +Blanc09 blank +--------------------------- ------------ ------------ Output files ------------ -xset.merged.RData: rdata.xcms.raw format +xset.merged.RData: rdata.xcms.findchrompeaks format | Rdata file that is necessary in the next step of the workflow "xcms.group".