view align_samples.xml @ 1:a941ec0fd2a4 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06

<tool id="dimspy_align_samples" name="Align Samples" version="1.0.0">
    <description> - Align peaks across Peaklists</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        dimspy align-samples
        --input '$hdf5_file_in'
        --output '$hdf5_file_out'
        #if $filelist
            --filelist '$filelist'
        #end if
        --ppm $ppm
        #if $hdf5_to_txt.standard
            &&
            @HDF5_PM_TO_TXT@
        #end if
        #if $hdf5_to_txt.comprehensive
            &&
            @HDF5_PM_TO_TXT_COMPREHENSIVE@
        #end if
    ]]>
    </command>
    <inputs>
        <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="" argument="--input"/>
        <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for  Process Scans or Replicate Filter." argument="--filelist"/>
        <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." argument="--ppm"/>
        <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
        <expand macro="hdf5_pm_to_txt" />
    </inputs>
    <outputs>
        <expand macro="outputs_peak_intensity_matrix" />
    </outputs>
    <tests>
        <test>
            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
            <param name="ppm" value="2.0"/>
            <param name="delimiter" value="tab"/>
            <param name="hdf5_to_txt|standard" value="True"/>
            <param name="hdf5_to_txt|comprehensive" value="False"/>
            <param name="hdf5_to_txt|samples_representations" value="rows"/>
            <param name="hdf5_to_txt|matrix_attr" value="intensity"/>
            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv" compare="sim_size"/>
        </test>
        <test>
            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
            <param name="ppm" value="2.0"/>
            <param name="delimiter" value="tab"/>
            <param name="hdf5_to_txt|standard" value="True"/>
            <param name="hdf5_to_txt|comprehensive" value="False"/>
            <param name="hdf5_to_txt|representation_samples" value="columns"/>
            <param name="hdf5_to_txt|matrix_attr" value="intensity"/>
            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as_t.txt" ftype="tsv" compare="sim_size"/>
        </test>
        <test>
            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
            <param name="ppm" value="2.0"/>
            <param name="delimiter" value="tab"/>
            <param name="hdf5_to_txt|standard" value="True"/>
            <param name="hdf5_to_txt|comprehensive" value="True"/>
            <param name="hdf5_to_txt|samples_representations" value="rows"/>
            <param name="hdf5_to_txt|matrix_attr" value="mz"/>
            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as_mz.txt" ftype="tsv" compare="sim_size"/>
            <output name="matrix_comprehensive_file_out" file="peak_matrix_as_mz_compr.txt" ftype="tsv" compare="sim_size"/>
        </test>
    </tests>
    <help>
-------------
Align Samples
-------------

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

| Use this tool to align Peaklists according to their constituent mass spectral peaks. 
| In the DIMS analysis workflow, align samples typically follows 'Replicate Filter'.
| This tool may, however, be used to align any Peaklists (e.g. aligning individual Peaklists for each replicate of a sample).

Parameters
----------

**\1. Set of Peaklists (HDF5 file)** (REQUIRED)

For the default DIMS analysis workflow, this comprises a set of Peaklists output from the sequential application of the  'process_scans' tools, followed by the 'replicate_filter' tool.

	
**\2. Filelist / Samplelist** (OPTIONAL)
   
| A tabular-formatted .txt file with columns: filename, batch, classLabel, injectionOrder.
| Additional collumns are allowed but are not used during processing.
| This file must be uploaded in to (or available from) the current history in order to allow for it to be selected from the drop-down menu.
| **NOTE:** Only provide a filelist if you like to exclude Peaklist, update the metadata (e.g. classLabel), or if you have not provided a filelist for 'Process Scans' or Replicate Filter'.
| 
	
<![CDATA[
	
		+-------------------------------+-------+------------+----------------+
		| filename                      | batch | classLabel | injectionOrder |
		+-------------------------------+-------+------------+----------------+
		| sample_rep1_rep3_rep4         | 1     | sample     | 1              |
		+-------------------------------+-------+------------+----------------+
		| blank_rep1_rep2_rep3          | 1     | sample     | 2              |
		+-------------------------------+-------+------------+----------------+
		| ...                           | ...   | ...        | ...            |
		+-------------------------------+-------+------------+----------------+

]]>

**\3. ppm** (REQUIRED; default = 2.0)
   
| A numeric value from 0 upwards.
| Peaks with m/z differences (measured in parts-per-million) below this value are clustered together as a single feature. 
|

@help_options_addtional_output@

@github_developers_contributors@

    </help>
    <expand macro="citations" />
</tool>