view metaquantome_sample.xml @ 6:094779c6cdaa draft

planemo upload

<?xml version='1.0' encoding='utf-8'?>
<tool id="sample" name="metaQuantome: create samples file" version="@VERSION@.3">
    <description></description>
    <macros>
        <token name="@VERSION@">1.1.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">megahit</requirement>
    </requirements>
    <version_command>megahit --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #set $samp_header = 'group\tcolnames'
        echo -e '${samp_header}' > samp_file.tab;
        #if $samps_args.samps_src == 'build':
            #for $s in $samps_args.samps
                #set $sample = str($s.group_name) + '\t' + str($s.col_names)
                echo -e '${sample}' >> samp_file.tab;
            #end for
        #else:
            #for $s in $samps_args.samps
                cat ${samps_args.file} | cut -f ${s.col_names} |
                head -n 1 | tr '\t' ',' |
                cat <(echo -e -n "${s.group_name}\t") - >> samp_file.tab;
            #end for
        #end if
    ]]></command>
    <inputs>
        <conditional name="samps_args">
            <param name="samps_src" type="select" label="Sample file creation method">
                <option value="build">Specify samples</option>
                <option value="history">Select samples from existing file's header</option>
            </param>
            <when value="build">
                <repeat name="samps" title="Samples">
                    <param name="group_name" type="text" label="Group name" />
                    <param name="col_names" type="text" label="Column" help="Specify the column names of the sample file. Use commas to separate multiple columns." />
                </repeat>
            </when>
            <when value="history">
                <param name="file" type="data" format="tabular" label="File with group name headers" help="Ex: moFF tool output (headers: peptide X737NS X737WS)" />
                <repeat name="samps" title="Samples">
                    <param name="group_name" type="text" label="Group name" />
                    <param name="col_names" type="data_column" multiple="true" data_ref="file" label="Column" help="Specify the column indices of the file's header" />
                </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="samples_file" from_work_dir="samp_file.tab" label="${tool.name}  ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="samps_src" value="build" />
            <repeat name="samps">
                <param name="group_name" value="NS"/>
                <param name="col_names" value="X737NS,X852NS,X867NS"/>
            </repeat>
            <repeat name="samps">
                <param name="group_name" value="WS"/>
                <param name="col_names" value="X737WS,X852WS,X867WS"/>
            </repeat>
            <output name="samples_file" file="samples.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="samps_src" value="history" />
            <param name="file" value="int_737_test.tab" ftype="tabular" />
            <repeat name="samps">
                <param name="group_name" value="NS"/>
                <param name="col_names" value="3,5,7"/>
            </repeat>
            <repeat name="samps">
                <param name="group_name" value="WS"/>
                <param name="col_names" value="2,4,6"/>
            </repeat>
            <output name="samples_file" file="samples.tab" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
metaQuantome: create samples file
===================

The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify which column names are affilated with which experimental groups. 

*Create samples file*

    =====  ====================
    group  colnames   
    =====  ====================
    NS     X737NS,X852NS,X867NS  
    WS     X737WS,X852WS,X867WS
    =====  ==================== 


There are two methods for generating this input file:

1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*). 

2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 1, 3, and 5 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.

*Example int.tab file*
============ ====== ======  ======  ======  ======  ====== 
peptide      X737WS X737NS  X852WS  X852NS  X867WS  X867NS
============ ====== ======  ======  ======  ======  ======
LPGQQHGTPSAK 1      2       3       4       5       6
ELPGLAALTDK  7      8       9       10      11      12
============ ====== ======  ======  ======  ======  ======


Questions, Comments, Problems, Kudos
------------------------------------

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv033</citation>
    </citations>
</tool>