| Previous changeset 5:df7b3b846cb6 (2016-03-18) Next changeset 7:ed8d80fc927c (2016-04-25) |
|
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 |
|
modified:
README.rst abims_xcms_summary.xml tool_dependencies.xml xcms_summary.r |
|
added:
macros.xml planemo_test.sh |
|
removed:
planemo.sh |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 README.rst --- a/README.rst Fri Mar 18 10:44:23 2016 -0400 +++ b/README.rst Fri Apr 08 10:40:12 2016 -0400 |
| b |
| @@ -2,7 +2,22 @@ Changelog/News -------------- +**Version 1.0.1 - 04/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + **Version 1.0.0 - 10/02/2016** - NEW: Create a summary of XCMS analysis + +Test Status +----------- + +Planemo test using conda: failed + +Planemo test using source env.sh: passed + +Planemo shed_test : passed + |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 abims_xcms_summary.xml --- a/abims_xcms_summary.xml Fri Mar 18 10:44:23 2016 -0400 +++ b/abims_xcms_summary.xml Fri Apr 08 10:40:12 2016 -0400 |
| [ |
| @@ -1,20 +1,21 @@ -<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0"> +<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.1"> <description>Create a summary of XCMS analysis</description> - + + <macros> + <import>macros.xml</import> + </macros> + <requirements> <requirement type="package" version="3.1.2">R</requirement> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="1.44.0">xcms</requirement> - <requirement type="package" version="1.22.0">camera</requirement> + <requirement type="package" version="1.22.0">bioconductor-camera</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> + <expand macro="stdio"/> - <command interpreter="Rscript"><![CDATA[ - xcms_summary.r + <command><![CDATA[ + $__tool_directory__/xcms_summary.r image $image htmlOutput $htmlOutput @@ -35,19 +36,13 @@ <tests> <test> <param name="image" value="fillpeaks.RData" /> - <output name="htmlOutput" file="summary.html" ftype="html" /> + <output name="htmlOutput" file="summary.html" /> </test> </tests> <help><![CDATA[ - -.. class:: infomark - -**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M] - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - ---------------------------------------------------- + +@HELP_AUTHORS@ ============ Xcms.summary @@ -65,6 +60,11 @@ Changelog/News -------------- +**Version 1.0.1 - 04/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + **Version 1.0.0 - 10/02/2016** - NEW: Create a summary of XCMS analysis @@ -73,8 +73,6 @@ ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + <expand macro="citation" /> </tool> |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Apr 08 10:40:12 2016 -0400 |
| [ |
| @@ -0,0 +1,51 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.44.0">bioconductor-xcms</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_XCMS_SCRIPT@"> + LANG=C Rscript $__tool_directory__/xcms.r + </token> + + <token name="@COMMAND_LOG_EXIT@"> + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + </token> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + + </token> + + + <xml name="citation"> + <citations> + <citation type="doi">10.1021/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 planemo.sh --- a/planemo.sh Fri Mar 18 10:44:23 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_summary --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS analysis" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nThis tool create a HTML summary of XCMS analysis" --category="Metabolomics" |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Fri Apr 08 10:40:12 2016 -0400 |
| [ |
| @@ -0,0 +1,21 @@ +planemo conda_init +planemo conda_install . +#Linking packages ... +#Error: ERROR: placeholder '/root/miniconda3/envs/_build_placehold_placehold_placehold_placehold_placehold_p' too short in: ncurses-5.9-4 + + + +source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh +source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh +planemo test --install_galaxy + +#All 1 test(s) executed passed. +#abims_xcms_summary[0]: passed + + +planemo shed_test --install_galaxy --galaxy_branch "dev" + +#All 2 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[0]: passed +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[1]: passed + |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 tool_dependencies.xml --- a/tool_dependencies.xml Fri Mar 18 10:44:23 2016 -0400 +++ b/tool_dependencies.xml Fri Apr 08 10:40:12 2016 -0400 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.1.2"> - <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="camera" version="1.22.0"> + <package name="bioconductor-camera" version="1.22.0"> <repository changeset_revision="845eb883bd1b" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
| b |
| diff -r df7b3b846cb6 -r ca7c9a6da2c6 xcms_summary.r --- a/xcms_summary.r Fri Mar 18 10:44:23 2016 -0400 +++ b/xcms_summary.r Fri Apr 08 10:40:12 2016 -0400 |
| b |
| @@ -1,5 +1,5 @@ -#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file -# version="0.1.0" +#!/usr/bin/env Rscript +# version="1.0.0" #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM |