Mercurial > repos > lecorguille > xcms_retcor
changeset 4:ac93ed26e4e1 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
| author | lecorguille |
|---|---|
| date | Mon, 04 Jul 2016 08:46:17 -0400 |
| parents | 3b44991a8e05 |
| children | fc576e3c1a92 |
| files | abims_xcms_retcor.xml macros.xml planemo_test.sh tool_dependencies.xml |
| diffstat | 4 files changed, 41 insertions(+), 17 deletions(-) [+] |
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--- a/abims_xcms_retcor.xml Mon Apr 25 11:14:51 2016 -0400 +++ b/abims_xcms_retcor.xml Mon Jul 04 08:46:17 2016 -0400 @@ -32,9 +32,9 @@ plottype $methods.options.plottype #end if #end if - #if $zip_file: - zipfile $zip_file - #end if + + @COMMAND_ZIPFILE_LOAD@ + @COMMAND_LOG_EXIT@ ]]></command> @@ -81,8 +81,9 @@ </conditional> </when> </conditional> - <!-- To pass planemo test --> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> + + <expand macro="zipfile_load"/> + </inputs> <outputs> @@ -109,7 +110,8 @@ <param name="methods|options|span" value="0.2"/> <param name="methods|options|family" value="gaussian"/> <param name="methods|options|plottype" value="deviation"/> - <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> + <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> + <param name="zipfile_load_conditional|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> <output name="log"> <assert_contents> <has_text text="object with 4 samples" /> @@ -131,7 +133,8 @@ <param name="methods|options|span" value="0.2"/> <param name="methods|options|family" value="gaussian"/> <param name="methods|options|plottype" value="deviation"/> - <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> + <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> <output name="log"> <assert_contents> <has_text text="object with 4 samples" />
--- a/macros.xml Mon Apr 25 11:14:51 2016 -0400 +++ b/macros.xml Mon Jul 04 08:46:17 2016 -0400 @@ -3,9 +3,9 @@ <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> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> </xml> <xml name="stdio"> @@ -26,6 +26,30 @@ sh -c "exit \$return" </token> + <!-- zipfile load for planemo test --> + + <token name="@COMMAND_ZIPFILE_LOAD@"> + #if $zipfile_load_conditional.zip_file: + zipfile $zipfile_load_conditional.zip_file + #end if + </token> + + <xml name="zipfile_load"> + <conditional name="zipfile_load_conditional"> + <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" selected="peakgroups">yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> + </when> + </conditional> + </xml> + + + <token name="@HELP_AUTHORS@"> .. class:: infomark
--- a/planemo_test.sh Mon Apr 25 11:14:51 2016 -0400 +++ b/planemo_test.sh Mon Jul 04 08:46:17 2016 -0400 @@ -1,13 +1,10 @@ # Example of planemo command to launch test -# Note: --galaxy_branch "dev" is set to deal with zip file - - # -- Use of installed package environments # after having installing package on a local galaxy instance 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-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh -planemo test --install_galaxy --galaxy_branch "dev" +planemo test --install_galaxy #All 1 test(s) executed passed. #abims_xcms_retcor[0]: passed @@ -16,7 +13,7 @@ # -- Use of conda dependencies planemo conda_init --conda_prefix /tmp/mc planemo conda_install --conda_prefix /tmp/mc . -planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution #All 1 test(s) executed passed. #abims_xcms_retcor[0]: passed
--- a/tool_dependencies.xml Mon Apr 25 11:14:51 2016 -0400 +++ b/tool_dependencies.xml Mon Jul 04 08:46:17 2016 -0400 @@ -3,7 +3,7 @@ <package name="R" version="3.1.2"> <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="bioconductor-xcms" version="1.44.0"> - <repository changeset_revision="58ebb405a3d6" name="package_bioconductor_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="bioconductor-xcms" version="1.46.0"> + <repository changeset_revision="779207ed5674" name="package_bioconductor_xcms_1_46_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>