Mercurial > repos > lecorguille > xcms_export_samplemetadata

view xcms_export_samplemetadata.xml @ 10:cdab04a1d1d7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:14:35 +0000
parents 94eb263cfab4
children
line wrap: on
line source

<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>