comparison normalisation.xml @ 7:76dcbe930b1d draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"

6:192cac570229

# 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="3.2.3.1">
        <description>Normalise OTUs abundance.</description>
        <requirements>
                <requirement type="package" version="3.2.3">frogs</requirement>
        </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." />

            <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
        </test>
    </tests>
	<help>

.. image:: static/images/FROGS_logo.png 
   :height: 144
   :width: 110


.. class:: infomark page-header h2

What it does

**Sequence file**:

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

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

.. class:: h3

Outputs

Advices

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


----

**Contact**

Contacts: [e-mail]

Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers

Website: http://frogs.toulouse.inrae.fr/

Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_

	</help>
</tool>

7:76dcbe930b1d

# 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." />

            <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
        </test>
    </tests>
	<help>

@HELP_LOGO@

.. class:: infomark page-header h2

What it does

**Sequence file**:

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

**Abundance file**:

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

.. class:: h3

Outputs

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>