Mercurial > repos > peterjc > venn_list
changeset 17:f606fe0b1250 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 00fbc0df3b4065b501409402979d702164bf0165
| author | peterjc |
|---|---|
| date | Tue, 12 May 2015 10:50:20 -0400 |
| parents | 493c0fa29239 |
| children | 7440116e24e5 |
| files | tools/venn_list/README.rst tools/venn_list/venn_list.xml |
| diffstat | 2 files changed, 39 insertions(+), 11 deletions(-) [+] |
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--- a/tools/venn_list/README.rst Tue May 12 10:49:36 2015 -0400 +++ b/tools/venn_list/README.rst Tue May 12 10:50:20 2015 -0400 @@ -69,6 +69,9 @@ - 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). ======= ======================================================================
--- a/tools/venn_list/venn_list.xml Tue May 12 10:49:36 2015 -0400 +++ b/tools/venn_list/venn_list.xml Tue May 12 10:50:20 2015 -0400 @@ -1,4 +1,4 @@ -<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> @@ -53,22 +53,47 @@ <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>