isa2w4m.xml

<!-- vi: se fdm=marker : -->
<tool id="isa2w4m" name="ISA to W4M" version="1.1.3">

	<description>Convert ISA data type into W4M format</description>

	<requirements>
		<requirement type="package" version="1.2.5">pandas</requirement>
		<requirement type="package" version="0.12.2">isatools</requirement>
	</requirements>

	<!-- Command {{{1 -->

	<command><![CDATA[
		## @@@BEGIN_CHEETAH@@@

		$__tool_directory__/isa2w4m.py
		-i '$isa.extra_files_path'
		-s '$w4m_sample_metadata'
		-v '$w4m_variable_metadata'
		-m '$w4m_data_matrix'

		## Choose study to output
		#if $study:
			-n '$study'
		#end if

		## Choose assay to output
		#if $assay:
			-f '$assay'
		#end if

		## Filtering
		#if $sample_na_filtering:
			-S '$sample_na_filtering'
		#end if
		#if $variable_na_filtering:
			-V '$variable_na_filtering'
		#end if

		## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if
		## it sees just one character on stderr.
		2>&1

		## @@@END_CHEETAH@@@
	]]></command>

	<!-- Inputs {{{1 -->

	<inputs>
		<param name="isa" label="ISA" type="data" format="isa-tab"/>
		<param name="study" type="text" size="256" value="" help="Type here the name of the assay file you want to extract from the ISA archive. If unset, the first listed study will be used."/>
		<param name="assay" type="text" size="256" value="" help="Type here the name of the study file you want to extract from the ISA archive. If unset, the first listed assay in the study will be used"/>
		<param name="sample_na_filtering" type="text" label="Sample metadata columns NA filtering" help="The rows that contain NA value in the specified columns will be filtered out. Column names must be separated by commas."/>
		<param name="variable_na_filtering" type="text" label="Variable metadata columns NA filtering" help="The rows that contain NA value in the specified columns will be filtered out. Column names must be separated by commas."/>
	</inputs>

	<!-- Outputs {{{1 -->

    <outputs>
		<data name="w4m_variable_metadata" label="${isa.name} W4M var" format="tabular"/>
        <data name="w4m_sample_metadata" label="${isa.name} W4M samp" format="tabular"/>
        <data name="w4m_data_matrix" label="${isa.name} W4M data" format="tabular"/>
	</outputs>

	<!-- Tests {{{1 -->
	<tests>
		<test>
			<param name="isa" value="MTBLS30.zip" ftype="isa-tab"/>
			<output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/>
			<output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/>
			<output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/>
		</test>
		<test>
			<param name="isa" value="MTBLS174.zip" ftype="isa-tab"/>
			<output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/>
			<output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/>
			<output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/>
		</test>
	</tests>

	<!-- Help {{{1 -->
    <help>
<!-- @@@BEGIN_RST@@@ -->

====================
ISA to W4M converter
====================

Converts an ISA-Tab dataset into W4M 3 files format.

------
Inputs
------

ISA dataset
===========

The ISA-Tab dataset to convert to W4M format.

Study to extract
================

The file name of the study to extract from the ISA dataset.

Assay to extract
================

The file name of the assay to extract from the ISA dataset chosen study.

Sample NA filtering
===================

This is a comma separated list of column names from the sample metadata dataset.
Rows containg NA values in one or more of the listed columns will be removed from the dataset.

Variable NA filtering
=====================

This is a comma separated list of column names from the variable metadata dataset.
Rows containg NA values in one or more of the listed columns will be removed from the dataset.

-------
Outputs
-------

The output is a set of 3 datasets:

 - Samples metadata.
 - Variables metadata.
 - Samples x variables matrix. 

<!-- @@@END_RST@@@ -->
    </help>

	<!-- Citations {{{1 -->
    <citations>
        <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
        <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
    </citations>

</tool>