Mercurial > repos > oinizan > frogs_2_0_0
changeset 15:9922f7908f3c draft
planemo upload commit 3305cccdb02c7c2f76d7420959e189f19cc4d214-dirty
| author | oinizan |
|---|---|
| date | Wed, 17 Oct 2018 05:51:05 -0400 |
| parents | 0f28ff7dc19b |
| children | fc37dfd723e7 |
| files | r_manova.xml upload_tar.xml |
| diffstat | 2 files changed, 1 insertions(+), 93 deletions(-) [+] |
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--- a/r_manova.xml Wed Oct 17 05:46:24 2018 -0400 +++ b/r_manova.xml Wed Oct 17 05:51:05 2018 -0400 @@ -16,6 +16,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. --> <tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="1.0.0"> + <description>perform Multivariate Analysis of Variance (MANOVA)</description> <requirements> <requirement type="package" version="2.0.1">frogs</requirement> </requirements>
--- a/upload_tar.xml Wed Oct 17 05:46:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -<?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>