comparison normalisation.xml @ 9:7bf54edaba24 draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty

8:348387ffe793

# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-->
<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy2">
        <description>Normalise OTUs abundance.</description>

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

    <expand macro="requirements"/>

        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>
		normalisation.py
		                       --input-biom '$input_biom'
		                       --input-fasta '$input_fasta'
		                       --num-reads $num_reads
		                       --output-biom '$output_biom'
		                       --output-fasta '$output_fasta'
		                       --summary-file '$summary_file'
	</command>
	<inputs>
		<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
		<param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
	</inputs>
	<outputs>
		<data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
		<data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" />
		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
	</outputs>
    <tests>
        <test>
            <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/>
	        <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
        	<param name="num_reads" value="100"/>
            <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
            <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
            <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
        </test>
    </tests>

**Abundance file**:

The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).

.. class:: h3

Outputs

**Sequence file** (normalised_seed.fasta):

 The normalised sequences file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).

**Abundance file** (normalised_abundance.biom):

 The normalised abundance file (format `BIOM <http://biom-format.org/>`_).

**Summary file** (report.html):

 Information about discarded data (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).


.. class:: infomark page-header h2

Advices

The number specified in "Number of reads" must be smaller than each total number of sequences by sample.


@HELP_CONTACT@

	</help>

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

9:7bf54edaba24

# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-->
<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
        <description>Normalise OTUs abundance.</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>
		which normalisation.py;

		normalisation.py 
		                       --input-biom '$input_biom'
		                       --input-fasta '$input_fasta'
		                       #if $sampling_method.sampling_by_min == "yes"
		                       	 --sampling-by-min
		                       #else
		                         --num-reads $sampling_method.num_reads
		                       	 #if $sampling_method.delete_samples
		                           --delete-samples
		                         #end if
		                       #end if
		                       --output-biom '$output_biom'
		                       --output-fasta '$output_fasta'
		                       --summary-file '$summary_file'
	</command>
	<inputs>
		<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
		<conditional name="sampling_method">
			<param name="sampling_by_min" type="select" label="Sampling method" help='Sampling by the number of sequences of the smallest sample, or select a number manually' display='radio'>
            	<option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option>
            	<option value="no">Select a number of reads</option>
			</param>
		<when value="no">
			<param name="num_reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
			<param name="delete_samples" type="boolean" label="Remove samples that have an initial number of reads below the number of reads to sample ?"  />
		</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
		<data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" />
		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
	</outputs>
    <tests>
        <test>
            <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/>
	        <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
        	<conditional name="sampling_method">
        	<param name="sampling_by_min" value="true"/>
        	</conditional>
            <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
            <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
            <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
        </test>
    </tests>

**Abundance file**:

The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).

**Sampling method**:

Sequence normalisation method :

 - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of reads of the smallest sample, and selects this number for all other samples.
 - **Select number of reads** : Manually select a number of reads.

.. image:: static/images/icon_warning_sml.gif 

If the **remove samples** option is enabled, samples whose total number of sequences is lower than the specified number will be removed inside the abundance table. 
If the option is disabled, the samples will be kept in the analysis but with a number of sequences lower than the specified number (the total number of the sample).

.. class:: h3

Outputs

**Sequence file** (normalised_seed.fasta):

 The normalised sequences file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).

**Abundance file** (normalised_abundance.biom):

 The normalised abundance file. If option **remove samples** has been chosen, then the abundance table will no longer contain information about the removed samples. (format `BIOM <http://biom-format.org/>`_).

**Report file** (report.html):

 Information about discarded data (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).


.. class:: infomark page-header h2


@HELP_CONTACT@

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