Migrating the generic_filter tool to tools-repository

tools/generic_filter/.shed.yml

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+categories: [Metabolomics]
+description: '[W4M][Utils] Filtering according to specific variables'
+homepage_url: http://workflow4metabolomics.org
+remote_repository_url: https://github.com/workflow4metabolomics/tools-metabolomics
+long_description: 'Part of the W4M project: http://workflow4metabolomics.org / The
+  R script removes all samples and/or variables corresponding to specific values 
+  regarding designated factors or numerical variables, in datasets corresponding to 
+  dataMatrix, sampleMetadata and variableMetadata.'
+name: generic_filter
+owner: melpetera

tools/generic_filter/.travis.yml

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+# This is a special configuration file to run tests on Travis-CI via
+# GitHub notifications when changes are committed.
+#
+# See http://travis-ci.org/ for details
+language: python
+
+before_install:
+ - sudo apt-get install -y python-virtualenv
+ - virtualenv planemo-venv
+ - . planemo-venv/bin/activate
+ - pip install --upgrade pip setuptools
+ - pip install planemo
+ - planemo conda_init
+
+install:
+ - planemo conda_install ${TRAVIS_BUILD_DIR}
+
+script:
+- planemo test --install_galaxy --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}

tools/generic_filter/Dockerfile

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+################################################################################
+### 
+### [CONTAINER CORE FUNCTIONS]: 
+###     install "Tool - Generic Filter" Galaxy tool (and required third part softwares, libraries, ...).
+### [NOTE]
+###     please refer to README.md and about_docker.md files for further informations
+### 
+################################################################################
+
+################################################################################
+### fix parent containter
+FROM ubuntu:16.04
+
+################################################################################
+### set author
+MAINTAINER Nils Paulhe <[email protected]>
+
+################################################################################
+### sets the environment variables
+ENV TOOL_VERSION = "release_2016.03.03"
+ENV CONTAINER_VERSION = 0.1
+
+LABEL version = "${CONTAINER_VERSION}"
+LABEL tool_version = "${TOOL_VERSION}"
+
+################################################################################
+### install third part tools 
+
+# add debian repo for latest version of R
+RUN echo "deb http://cran.univ-paris1.fr/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list && \
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 
+
+# Update and upgrade system
+RUN apt-get update && \
+    apt-get -y upgrade
+
+# install R
+RUN apt-get install -y \ 
+    r-base \
+    libcurl4-openssl-dev \
+    libxml2-dev
+# NOTE: add `apt-get install -y git` if required
+
+# init R env. (Docker)
+RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
+
+# install R libs
+RUN Rscript -e "install.packages('batch', dep=TRUE)"
+
+################################################################################
+### install core scripts
+
+# init. WORKDIR
+RUN [ "mkdir", "/scripts" ]
+
+#
+# [NOTE] to add scripts, we have two options: get them from GitHub OR copy them from this directory
+# 
+
+# get scripts using Git (option 1)
+# RUN cd /scripts && \
+#    git clone -b release/${TOOL_VERSION} --recursive https://github.com/workflow4metabolomics/tool-generic_filter.git
+
+# copy scripts files from this directory (option 2)
+COPY "." "/scripts/"
+
+## set WORKDIR
+# WORKDIR "/scripts"
+
+# set authorizations
+RUN ["chmod", "a+x", "/scripts/filter_wrap.R"]
+
+# make tool accessible through PATH
+ENV PATH = $PATH:/scripts
+
+################################################################################
+### clean
+RUN apt-get clean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}/ /tmp/* /var/tmp/*
+# NOTE: run `apt-get remove -y git && \` if required
+
+################################################################################
+### Define Entry point script
+## ENTRYPOINT ["/scripts/filter_wrap.R"]
+
+### [END]

tools/generic_filter/README.md

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+Generic Filter
+=======
+
+Metadata
+-----------
+
+ * **@name**: Generic Filter
+ * **@version**: 2020.01
+ * **@authors**: Marion Landi and Melanie Petera for first version - Maintainer: Melanie Petera (PFEM ; INRAE ; MetaboHUB)
+ * **@init date**: 2014, december
+ * **@main usage**: This tool allows to remove all samples and/or variables corresponding to specific values regarding designated factors or numerical variables. 
+
+
+Context
+-----------
+
+This tool is provided as one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance utilities. W4M is a French infrastructure providing software tools to process, analyse and annotate metabolomics data. 
+
+User interface is based on the Galaxy platform (homepage: https://galaxyproject.org/). It is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
+
+
+Configuration
+-----------
+
+### Requirement:
+ * R software: version > 3.0.0 recommended
+ * Specific R library: 'batch'
+
+### Docker:
+ * Use of this tool in a docker context:
+Information is provided in the [about_docker.md file](about_docker.md).
+
+
+Technical description
+-----------
+
+Main files:
+
+- filter_script.R: R function (core script)
+- filter_wrap.R: R script to link the main R function to inputs
+- generic_filter.xml: XML wrapper (interface for Galaxy)
+
+
+Services provided
+-----------
+
+ * Help and support: [email protected]
+
+
+License
+-----------
+
+ * Cea Cnrs Inria Logiciel Libre License, version 2.1 (CECILL-2.1)

tools/generic_filter/about_docker.md

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+# Tool - Generic Filter [Dockerfile]
+
+
+## Metadata
+
+- **@authors**: Nils Paulhe <[email protected]> (Only the docker part)
+- **@date creation**: `2017-09-04`
+- **@main usage**: create a Docker environment / container for "Tool - Generic Filter"
+
+## About
+
+For all informations about the tool please refer to its [README file](README.md). 
+For further information about Workflow4Metabolomics project and the people involved, please refer to [workflow4metabolomics.org](http://workflow4metabolomics.org/), [W4M github](https://github.com/workflow4metabolomics/) and [W4M Docker Hub](https://hub.docker.com/r/workflow4metabolomics/). 
+
+## Configuration
+
+### Requirement:
+ * Docker Engine, Docker skills
+ * a Galaxy server docker compliant
+
+### Warning:
+ * These scripts are provided WITHOUT ANY WARRANTY. 
+ * These scripts should be run by a system administrator (expert).
+
+## Services provided
+
+Build a docker container for "Tool - Generic Filter" Galaxy Tool.
+Provide a XML Galaxy wrapper: generic_filter.docker.xml
+
+## Technical description
+
+### Create the docker container
+
+``` bash
+docker build -t workflow4metabolomics/tool-generic_filter:2017.06 .
+```
+
+### Add the tool in Galaxy
+
+Note: the files name and path are just examples. Adapt them to your own Galaxy configuration / practices.
+
+If required, add in `config/job_conf.xml` file the minimal docker options:
+
+``` xml
+    <destinations default="docker_local">
+        <destination id="local" runner="local"/>
+        <destination id="docker_local" runner="local">
+          <param id="docker_enabled">true</param>
+          <param id="docker_sudo">false</param>
+       </destination>
+    </destinations>
+```
+
+For more options please refer to the [official documentation](https://galaxyproject.org/admin/tools/docker/).
+
+Copy or create a symbolic link of generic_filter.docker.xml file into your `tools/docker` directory (feel free to create or change the target directory). 
+Then add this XML resource in your `config/tool_conf.xml` file. For example:
+
+``` xml
+    <section id="docker_tools" name="Docker Tools">
+      <tool file="docker/generic_filter.docker.xml"/>
+    </section>
+```
+
+### Modify this tool's XML config. file
+
+replace these sections:
+```xml
+  <!-- requirements -->
+  <requirements>
+    <requirement type="package" version="1.1_4">r-batch</requirement>
+  </requirements>
+
+  <!-- cmd -->
+  <command>
+    Rscript '$__tool_directory__/filter_wrap.R'
+      dataMatrix_in "$dataMatrix_in"
+      sampleMetadata_in "$sampleMetadata_in"
+      <!-- ... -->
+```
+
+by these sections:
+```xml
+  <!-- requirements -->
+  <requirements>
+    <container type="docker">workflow4metabolomics/tool-generic_filter:2017.06</container>
+  </requirements>
+
+  <!-- cmd -->
+    /usr/bin/Rscript /scripts/filter_wrap.R
+      dataMatrix_in "$dataMatrix_in"
+      <!-- ... -->
+```
+
+## License (Dockerfile only!)
+
+The `Dockerfile` file is under the following license:
+```
+    Copyright (c) 2017 workflow4metabolomics.org / INRA
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+    SOFTWARE.
+```
+
+- For the Galaxy Tool's license, please refer to its `README` file. 
+- For the Galaxy Wrapper's license, please refer to its `XML` file.