Mercurial > repos > oinizan > frogs
changeset 1:5bd32b2feb20 draft
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 1745166eaaa0eac6c0690ad8f6bd0532ae3f3924"
| author | oinizan |
|---|---|
| date | Wed, 03 Mar 2021 17:24:12 +0000 |
| parents | 27f57425dc55 |
| children | ea386220db3c |
| files | FROGS_data_manager/data_manager_conf.xml FROGS_data_manager/tool-data/HVL_db.loc.sample FROGS_data_manager/tool-data/contaminant_db.loc FROGS_data_manager/tool-data/frogs_HVL_db.loc.sample FROGS_data_manager/tool-data/frogs_contaminant_db.loc FROGS_data_manager/tool_data_table_conf.xml.sample conda_toolshed_frogs |
| diffstat | 7 files changed, 82 insertions(+), 107 deletions(-) [+] |
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--- a/FROGS_data_manager/data_manager_conf.xml Wed Mar 03 17:03:54 2021 +0000 +++ b/FROGS_data_manager/data_manager_conf.xml Wed Mar 03 17:24:12 2021 +0000 @@ -2,7 +2,7 @@ <data_managers> <data_manager tool_file="data_manager/FROGS_data_manager.xml" id="frogs_data_manager"> <data_table name="frogs_db"> -<output> + <output> <column name="value" /> <column name="name" /> <column name="path" output_ref="output"> @@ -15,19 +15,5 @@ </column> </output> </data_table> - <data_table name="HVL_db"> - <output> - <column name="value"/> - <column name="name" /> - <column name="path" output_ref="output" > - <move type="file"> - <!--source>${path}/${value}.tsv</source--> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">HVL_db/</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/HVL_db/${value}.fasta</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> </data_manager> </data_managers>
--- a/FROGS_data_manager/tool-data/HVL_db.loc.sample Wed Mar 03 17:03:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -# Copyright (C) 2014 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/>. -# -# -#This is a sample file that enables tools FROGS_affiliations_postprocess to solve -#inclusive amplicon sequence by selecting the smallest reference among multihit -#You will need to create or download exact amplicon sequence reference fasta file -#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference -#Finally you will need to create HVL_db.loc file similar to this one in your galaxy -#tool-data directory.The HVL_db.loc file has this format (longer white space characters are -#TAB characters): -# -#<unique_database_name> <name> <file_path> -# -#First column will be the visible name in galaxy. -#So, for example, if you have UNITE 7.1 ITS1 (only!) stored -#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta -#then the HVL_db.loc entry would look like this: -# -# -# EXAMPLE FOR TEST : -#Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/HVL_db_data/Unite_extract_ITS1.fasta
--- a/FROGS_data_manager/tool-data/contaminant_db.loc Wed Mar 03 17:03:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -# Copyright (C) 2014 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/>. -# -# -#This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index. -#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants -#Finally you will need to create phiX_db.loc file similar to this one in your galaxy -#tool-data directory.The phiX_db.loc file has this format (longer white space characters are -#TAB characters): -# -#<contaminant_name> <name> <file_path> -# -#First column will be the visible name in galaxy. -#So, for example, if you had phix indexed stored in -#/galaxy_databanks/phiX/ -#then the phiX_db.loc entry would look like this: -# -# -# EXAMPLE FOR TEST : -#phiX_test phiX_test ${__HERE__}/phiX_db_data/phi.fa -# -#and your /galaxy_databanks/phiX/ directory -#would contain index files: -# -#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept. 2015 phi.fa -#-rw-rwxr-- 1 gpascal FROGS 132 16 sept. 2015 phi.fa.nhr -#-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin -#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq -#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FROGS_data_manager/tool-data/frogs_HVL_db.loc.sample Wed Mar 03 17:24:12 2021 +0000 @@ -0,0 +1,34 @@ +# Copyright (C) 2014 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/>. +# +# +#This is a sample file that enables tools FROGS_affiliations_postprocess to solve +#inclusive amplicon sequence by selecting the smallest reference among multihit +#You will need to create or download exact amplicon sequence reference fasta file +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference +#Finally you will need to create HVL_db.loc file similar to this one in your galaxy +#tool-data directory.The HVL_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<unique_database_name> <name> <file_path> +# +#First column will be the visible name in galaxy. +#So, for example, if you have UNITE 7.1 ITS1 (only!) stored +#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta +#then the HVL_db.loc entry would look like this: +# +# +# EXAMPLE FOR TEST : +#Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/HVL_db_data/Unite_extract_ITS1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FROGS_data_manager/tool-data/frogs_contaminant_db.loc Wed Mar 03 17:24:12 2021 +0000 @@ -0,0 +1,41 @@ +# Copyright (C) 2014 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/>. +# +# +#This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index. +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants +#Finally you will need to create phiX_db.loc file similar to this one in your galaxy +#tool-data directory.The phiX_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<contaminant_name> <name> <file_path> +# +#First column will be the visible name in galaxy. +#So, for example, if you had phix indexed stored in +#/galaxy_databanks/phiX/ +#then the phiX_db.loc entry would look like this: +# +# +# EXAMPLE FOR TEST : +#phiX_test phiX_test ${__HERE__}/phiX_db_data/phi.fa +# +#and your /galaxy_databanks/phiX/ directory +#would contain index files: +# +#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept. 2015 phi.fa +#-rw-rwxr-- 1 gpascal FROGS 132 16 sept. 2015 phi.fa.nhr +#-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin +#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq +#
--- a/FROGS_data_manager/tool_data_table_conf.xml.sample Wed Mar 03 17:03:54 2021 +0000 +++ b/FROGS_data_manager/tool_data_table_conf.xml.sample Wed Mar 03 17:24:12 2021 +0000 @@ -5,12 +5,12 @@ <columns>value, name, path</columns> <file path="tool-data/frogs_db.loc" /> </table> - <table name="HVL_db" comment_char="#"> + <table name="frogs_HVL_db" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/HVL_db.loc" /> + <file path="tool-data/frogs_HVL_db.loc" /> </table> - <table name="contaminant_db" comment_char="#"> + <table name="frogs_contaminant_db" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/contaminant_db.loc" /> + <file path="tool-data/frogs_contaminant_db.loc" /> </table> </tables>
--- a/conda_toolshed_frogs Wed Mar 03 17:03:54 2021 +0000 +++ b/conda_toolshed_frogs Wed Mar 03 17:24:12 2021 +0000 @@ -130,18 +130,7 @@ du owner description planemo shed_init # à compléter - planemo shed_create --shed_target testtoolshed # premier dépôt - planemo shed_update --shed_target testtoolshed # nouvelle release + planemo shed_create --shed_target testtoolshed # premier dépôt : dépôt frogs (sans nom de version a été créé lors de la mise en ligne de la version 3.2.1) + planemo shed_update --shed_target testtoolshed # nouvelle release : pour toutes les prochaines release il suffit de faire un update Dans .planemo.yml définition des login de compte toolshed, l'idée est de partager une clé pour pouvoir pousser à plusieurs. - -Pour 3.1.0: - proposer une data_table - - - -Ajout de l'affichage des versions des dépendances quand <tool>.py -h ==> comme ça la section test de la recette de conda, test l'install des python et les dépendances. -Check fonctionnement FROGS 3.0 avec la 1.1.b (beta version) -pandoc < 2.0 -est ce qu'on vire upload_tar? -correction des descriptions outils stat.