annotate xcms_merge.xml @ 2:3a5204f14fff draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298

<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.1.0">
    <description>Merge xcms.xcmsSet xset in one to be used by group</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements_light"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        Rscript $script_file
    ]]></command>

    <configfiles>
        <configfile name="script_file"><![CDATA[
suppressPackageStartupMessages(library(xcms, quietly=TRUE))

images=c(
"${"\",\"".join(map(str, $images))}"
)


cat("\tXSET MERGING...\n")

for(image in images) {
    load(image)
    cat(sampleNamesList\$sampleNamesOrigin,"\n")
    if (!exists("xset_merged")) {
        xset_merged=xset
        singlefile_merged=singlefile
        listOFlistArguments_merged=listOFlistArguments
        md5sumList_merged=md5sumList
        sampleNamesList_merged=sampleNamesList
    } else {
        xset_merged=c(xset_merged,xset)
        singlefile_merged=c(singlefile_merged,singlefile)
        listOFlistArguments_merged=c(listOFlistArguments_merged,listOFlistArguments)
        md5sumList_merged\$origin=rbind(md5sumList_merged\$origin,md5sumList\$origin)
        sampleNamesList_merged\$sampleNamesOrigin=c(sampleNamesList_merged\$sampleNamesOrigin,sampleNamesList\$sampleNamesOrigin)
        sampleNamesList_merged\$sampleNamesMakeNames=c(sampleNamesList_merged\$sampleNamesMakeNames,sampleNamesList\$sampleNamesMakeNames)
    }
}
rm(image)
xset=xset_merged; rm(xset_merged)
singlefile=singlefile_merged; rm(singlefile_merged)
listOFlistArguments=listOFlistArguments_merged; rm(listOFlistArguments_merged)
md5sumList=md5sumList_merged; rm(md5sumList_merged)
sampleNamesList=sampleNamesList_merged; rm(sampleNamesList_merged)

#if str($sampleMetadata) != 'None':
    cat("\tXSET PHENODATA SETTING...\n")
    sampleMetadata=read.table("$sampleMetadata", h=F, sep=";", stringsAsFactors=F)
    if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep="\t", stringsAsFactors=F)
    if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep=",", stringsAsFactors=F)
    if (ncol(sampleMetadata) < 2) {
        error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"
        print(error_message)
        stop(error_message)
    }

    sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)]

    if (any(is.na(sampclass(xset)))) {
        sample_missing <- rownames(phenoData(xset))[is.na(sampclass(xset))]
        error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
        print(error_message)
        stop(error_message)
    }
#end if



cat("\tXSET OBJECT INFO\n")

print(xset@phenoData)
print(xset)

cat("\tSAVE RData\n")
save.image("$xsetRData")

        ]]></configfile>
    </configfiles>

    <inputs>
        <param name="images" type="data" format="rdata.xcms.raw,rdata" label="xset RData / xcms.xcmsSet file" help="output file from another xcms.xcmsSet" 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"/>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" />
    </outputs>

    <tests>
        <test>
            <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
            <assert_stdout>
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                <has_text text="Mass range: 200.1-600 m/z" />
                <has_text text="Peaks: 9251 (about 2313 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <test>
            <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
            <param name="sampleMetadata" value="sampleMetadata.tab" />
            <assert_stdout>
                <has_text text="ko15    KO" />
                <has_text text="ko16    KO" />
                <has_text text="wt15    WT" />
                <has_text text="wt16    WT" />
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                <has_text text="Mass range: 200.1-600 m/z" />
                <has_text text="Peaks: 9251 (about 2313 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>
        <test>
            <param name="images" value="MM8-xset.RData,MM14-xset.RData" />
            <assert_stdout>
                <has_text text="object with 2 samples" />
                <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
                <has_text text="Mass range: 117.0357-936.7059 m/z" />
                <has_text text="Peaks: 236 (about 118 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </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="sampleMetadata" value="sampleMetadata_missing.tab" />
            <expand macro="test_file_load_single"/>
            <assert_stderr>
                <has_text text="Those samples are missing in your sampleMetadata: ko16" />
            </assert_stderr>
        </test>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

===================
Xcms.xcmsSet Merger
===================

-----------
Description
-----------

This tool will allow you to run one xcms.xcmsSet process per sample in parallel and then to merge all RData images in one.
The result is then suitable for xcms.group.

You can provide a sampleMetadata table to attribute phenotypic value to your samples.


-----------------
Workflow position
-----------------

**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
------------------------- ----------------- ------------------- ----------
...                       ...               ...                 ...
========================= ================= =================== ==========


**Downstream tools**

+---------------------------+--------------------+-----------------+
| Name                      | Output file        | Format          |
+===========================+====================+=================+
|xcms.group                 | xset.RData         | rdata.xcms.raw  |
+---------------------------+--------------------+-----------------+

.. image:: xcms_merge_workflow.png

-----------
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          |
+---------------------------+-----------------------+

Example of a sampleMetadata:

+---------------------------+------------+
|HU_neg_028                 |   bio      |
+---------------------------+------------+
|HU_neg_034                 |   bio      |
+---------------------------+------------+
|Blanc04                    |   blank    |
+---------------------------+------------+
|Blanc06                    |   blank    |
+---------------------------+------------+
|Blanc09                    |   blank    |
+---------------------------+------------+

------------
Output files
------------

xset.merged.RData: rdata.xcms.raw format

    | Rdata file that is necessary in the next step of the workflow "xcms.group".

---------------------------------------------------

Changelog/News
--------------

**Version 1.0.1 - 13/02/2017**

- IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file


**Version 1.0.0 - 03/02/2017**

- NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group

    ]]></help>

    <expand macro="citation" />
</tool>