| Previous changeset 4:991342eca214 (2015-04-29) Next changeset 6:ea68a1a4c1d9 (2017-02-02) |
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Commit message:
v0.0.9 - Tool Shed dependency for rpy and limma |
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modified:
tools/venn_list/README.rst tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.xml |
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| diff -r 991342eca214 -r 26e35d5133a1 tools/venn_list/README.rst --- a/tools/venn_list/README.rst Wed Apr 29 11:00:41 2015 -0400 +++ b/tools/venn_list/README.rst Sat Oct 10 08:52:01 2015 -0400 |
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| @@ -18,9 +18,8 @@ ====================== This should be straightforward, Galaxy should automatically download the tool -and the Biopython dependency. - -You will still need to install the R/Bioconductor package limma. +and the Python dependencies Biopython and rpy, and the R/Bioconductor package +limma. Manual Installation @@ -69,6 +68,10 @@ - Fixed and improved error handling when rpy is not available. - Test output relaxed to cope with more variation in PDF output. - Declare Biopython dependency via the Tool Shed. +v0.0.9 - Test with three-way Venn diagram. + - Includes testing of failure mode. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Tool Shed dependency for rpy and limma (thanks to Björn Grüning). ======= ====================================================================== @@ -81,21 +84,30 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + ... + +or:: -Check this worked:: + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + ... + +To just build and check the tar ball, use:: - $ tar -tzf venn_list.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ + ... + $ tar -tzf shed_upload.tar.gz tools/venn_list/README.rst + tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.py tools/venn_list/venn_list.xml - tools/venn_list/tool_dependencies.xml test-data/magic.pdf + test-data/rhodopsin_proteins.fasta test-data/venn_list.tabular - test-data/rhodopsin_proteins.fasta Licence (MIT) |
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| diff -r 991342eca214 -r 26e35d5133a1 tools/venn_list/tool_dependencies.xml --- a/tools/venn_list/tool_dependencies.xml Wed Apr 29 11:00:41 2015 -0400 +++ b/tools/venn_list/tool_dependencies.xml Sat Oct 10 08:52:01 2015 -0400 |
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| @@ -1,5 +1,11 @@ <?xml version="1.0"?> <tool_dependency> + <package name="limma" version="3.25.3"> + <repository changeset_revision="b19c06e97bce" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="rpy" version="1.0.3"> + <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> <package name="biopython" version="1.65"> <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> |
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| diff -r 991342eca214 -r 26e35d5133a1 tools/venn_list/venn_list.xml --- a/tools/venn_list/venn_list.xml Wed Apr 29 11:00:41 2015 -0400 +++ b/tools/venn_list/venn_list.xml Sat Oct 10 08:52:01 2015 -0400 |
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| @@ -1,9 +1,11 @@ -<tool id="venn_list" name="Venn Diagram" version="0.0.8"> +<tool id="venn_list" name="Venn Diagram" version="0.0.9"> <description>from lists</description> <requirements> <requirement type="python-module">rpy</requirement> + <requirement type="python-module">Bio</requirement> + <requirement type="package" version="1.0.3">rpy</requirement> + <requirement type="package" version="3.25.3">limma</requirement> <requirement type="package" version="1.65">biopython</requirement> - <requirement type="python-module">Bio</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -53,22 +55,47 @@ <param name="set" value="rhodopsin_proteins.fasta"/> <param name="lab" value="Rhodopsins"/> <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> + <assert_stdout> + <has_line line="Doing 1-way Venn Diagram" /> + <has_line line="Total of 10 IDs" /> + <has_line line="6 in Rhodopsins" /> + </assert_stdout> </test> - <!-- Can't use more than one repeat value in tests (yet) <test> + <param name="type_select" value="implicit"/> + <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> + <param name="sets_0|lab" value="Rhodopsins"/> + <param name="sets_1|set" value="four_human_proteins.fasta"/> + <param name="sets_1|lab" value="Human"/> + <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> + <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> + <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> + <assert_stdout> + <has_line line="Doing 3-way Venn Diagram" /> + <has_line line="Inferred total of 10 IDs" /> + <has_line line="6 in Rhodopsins" /> + <has_line line="4 in Human" /> + <has_line line="1 in Human vs Rhodopsin BLAST" /> + </assert_stdout> + </test> + <test expect_failure="true" expect_exit_code="1"> <param name="type_select" value="explicit"/> <param name="main" value="venn_list.tabular" ftype="tabular"/> <param name="main_lab" value="Some Proteins"/> - <param name="count" value="3"/> - <param name="set" value="rhodopsin_proteins.fasta"/> - <param name="lab" value="Rhodopsins"/> - <param name="set" value="four_human_proteins.fasta"/> - <param name="lab" value="Human"/> - <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/> - <param name="lab" value="Human vs Rhodopsin BLAST"/> - <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> + <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> + <param name="sets_0|lab" value="Rhodopsins"/> + <param name="sets_1|set" value="four_human_proteins.fasta"/> + <param name="sets_1|lab" value="Human"/> + <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> + <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> + <assert_stdout> + <has_line line="Doing 3-way Venn Diagram" /> + <has_line line="Total of 10 IDs" /> + </assert_stdout> + <assert_stderr> + <has_text_matching expression="Unexpected ID sp|Q9BS26|ERP44_HUMAN in fasta file *" /> + </assert_stderr> </test> - --> </tests> <help> |