Mercurial > repos > oinizan > frogs_2_0_0
changeset 17:c3a1ffe20635 draft
planemo upload commit c6884165c0c7aabb0c4b7b391f7413b45a4684d1
| author | oinizan |
|---|---|
| date | Tue, 23 Oct 2018 09:27:54 -0400 |
| parents | fc37dfd723e7 |
| children | d019be26ebb4 |
| files | README.md affiliation_OTU.xml upload_tar.xml |
| diffstat | 3 files changed, 124 insertions(+), 34 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Thu Oct 18 08:15:12 2018 -0400 +++ b/README.md Tue Oct 23 09:27:54 2018 -0400 @@ -1,1 +1,19 @@ -# FROGS-wrappers +# FROGS-wrappers 2.0.0 + + FROGS 2.0.0 sources are here => [https://github.com/geraldinepascal/FROGS](https://github.com/geraldinepascal/FROGS) + +## Description + FROGS Galaxy Wrappers (for the Toolshed) for FROGS version 2.0.0 + +## License + GNU GPL v3 + +## Copyright + 2015 INRA + +## Citation + Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + +## Contact + frogs@inra.fr +
--- a/affiliation_OTU.xml Thu Oct 18 08:15:12 2018 -0400 +++ b/affiliation_OTU.xml Tue Oct 23 09:27:54 2018 -0400 @@ -25,21 +25,16 @@ <exit_code range=":-1" /> </stdio> <command> - #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + #set $reference_fasta_filename = str( $ref_file.fields.path ) affiliation_OTU.py --reference "${reference_fasta_filename}" - --input-biom $biom_abundance - --input-fasta $fasta_sequences - --output-biom $biom_affiliation - --summary $summary - --nb-cpus $nb_cpu - --java-mem $mem - #if $rdp + --input-biom $biom_abundance + --input-fasta $fasta_sequences + --output-biom $biom_affiliation + --summary $summary + --nb-cpus $nb_cpu + --java-mem $mem + #if $rdp --rdp #end if </command> @@ -47,25 +42,10 @@ <!-- JOB Parameter --> <param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param> <param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param> - <!-- Database Choice --> - - - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Load reference genome from"> - <option value="cached">Local cache</option> - <option value="history">History</option> - </param> - <when value="cached"> - <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> - <options from_data_table="frogs_db"> - </options> - <validator type="no_options" message="A built-in database is not available" /> - </param> - </when> - <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference genome" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> - </when> - </conditional> + <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> + <options from_data_table="frogs_db"></options> + <validator type="no_options" message="A built-in database is not available" /> + </param> <param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" /> <!-- Files --> <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/> @@ -77,7 +57,6 @@ </outputs> <tests> <test> - <param name="reference_source_selector" value="cached" /> <param name="ref_file" value="db"/> <param name="fasta_sequences" value="swarm.fasta"/> <param name="biom_abundance" value="swarm.biom"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/upload_tar.xml Tue Oct 23 09:27:54 2018 -0400 @@ -0,0 +1,93 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# 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_upload_tar" name="FROGS Upload archive" version="1.1.0" workflow_compatible="false"> + <description>from your computer</description> + <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + upload_tar.py --param-file $paramfile + #set $outnum = 0 + #while $varExists('output%i' % $outnum): + #set $output = $getVar('output%i' % $outnum) + #set $outnum += 1 + --output ${output.dataset.dataset.id}:${output.file_name} + #end while + </command> + <inputs nginx_upload="true"> + <param name="async_datasets" type="hidden" value="None"/> + <param name="file_type" type="hidden" label="File Format" help="Which format? See help below"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> + <column name="value" index="1"/> + <column name="name" index="0"/> + <filter type="sort_by" column="0"/> + <filter type="add_value" name="Auto-detect" value="auto" index="0"/> + </options> + </param> + <upload_dataset name="files" title="Specify Files for Dataset" metadata_ref="files_metadata"> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method."> + <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs --> + </param> + <param name="url_paste" type="text" size="35" label="URL" help="Here you may specify the archive URL."/> + <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/> + <param name="uuid" type="hidden" required="False" /> + <param name="to_posix_lines" type="hidden" value="Yes" /> + </upload_dataset> + </inputs> + <outputs> + </outputs> + <help> + +.. class:: infomark page-header h2 + +What it does + +Allow to upload a TAR archive as one dataset in Galaxy. + + +.. class:: infomark page-header h2 + +Advices + +To generate a TAR archive on windows, you can use `7zip <http://www.7-zip.org/>`_ and choose as archive format *tar* + +If your file is larger than 2GB, you need to upload your archive on a public server before indicating its public URL + +If you have access to a tool generating symbolic link on your Galaxy account, prefer this latest option in any cases. + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + </help> + <citations> + <citation type="doi">10.7287/peerj.preprints.386v1</citation> + </citations> +</tool>