Mercurial > repos > peterjc > venn_list
comparison tools/venn_list/venn_list.xml @ 5:26e35d5133a1 draft
v0.0.9 - Tool Shed dependency for rpy and limma
| author | peterjc |
|---|---|
| date | Sat, 10 Oct 2015 08:52:01 -0400 |
| parents | 991342eca214 |
| children | ea68a1a4c1d9 |
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| 4:991342eca214 | 5:26e35d5133a1 |
|---|---|
| 1 <tool id="venn_list" name="Venn Diagram" version="0.0.8"> | 1 <tool id="venn_list" name="Venn Diagram" version="0.0.9"> |
| 2 <description>from lists</description> | 2 <description>from lists</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="python-module">rpy</requirement> | 4 <requirement type="python-module">rpy</requirement> |
| 5 <requirement type="python-module">Bio</requirement> | |
| 6 <requirement type="package" version="1.0.3">rpy</requirement> | |
| 7 <requirement type="package" version="3.25.3">limma</requirement> | |
| 5 <requirement type="package" version="1.65">biopython</requirement> | 8 <requirement type="package" version="1.65">biopython</requirement> |
| 6 <requirement type="python-module">Bio</requirement> | |
| 7 </requirements> | 9 </requirements> |
| 8 <stdio> | 10 <stdio> |
| 9 <!-- Anything other than zero is an error --> | 11 <!-- Anything other than zero is an error --> |
| 10 <exit_code range="1:" /> | 12 <exit_code range="1:" /> |
| 11 <exit_code range=":-1" /> | 13 <exit_code range=":-1" /> |
| 51 <param name="main" value="venn_list.tabular" ftype="tabular"/> | 53 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
| 52 <param name="main_lab" value="Some Proteins"/> | 54 <param name="main_lab" value="Some Proteins"/> |
| 53 <param name="set" value="rhodopsin_proteins.fasta"/> | 55 <param name="set" value="rhodopsin_proteins.fasta"/> |
| 54 <param name="lab" value="Rhodopsins"/> | 56 <param name="lab" value="Rhodopsins"/> |
| 55 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> | 57 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> |
| 58 <assert_stdout> | |
| 59 <has_line line="Doing 1-way Venn Diagram" /> | |
| 60 <has_line line="Total of 10 IDs" /> | |
| 61 <has_line line="6 in Rhodopsins" /> | |
| 62 </assert_stdout> | |
| 56 </test> | 63 </test> |
| 57 <!-- Can't use more than one repeat value in tests (yet) | |
| 58 <test> | 64 <test> |
| 65 <param name="type_select" value="implicit"/> | |
| 66 <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> | |
| 67 <param name="sets_0|lab" value="Rhodopsins"/> | |
| 68 <param name="sets_1|set" value="four_human_proteins.fasta"/> | |
| 69 <param name="sets_1|lab" value="Human"/> | |
| 70 <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> | |
| 71 <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> | |
| 72 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> | |
| 73 <assert_stdout> | |
| 74 <has_line line="Doing 3-way Venn Diagram" /> | |
| 75 <has_line line="Inferred total of 10 IDs" /> | |
| 76 <has_line line="6 in Rhodopsins" /> | |
| 77 <has_line line="4 in Human" /> | |
| 78 <has_line line="1 in Human vs Rhodopsin BLAST" /> | |
| 79 </assert_stdout> | |
| 80 </test> | |
| 81 <test expect_failure="true" expect_exit_code="1"> | |
| 59 <param name="type_select" value="explicit"/> | 82 <param name="type_select" value="explicit"/> |
| 60 <param name="main" value="venn_list.tabular" ftype="tabular"/> | 83 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
| 61 <param name="main_lab" value="Some Proteins"/> | 84 <param name="main_lab" value="Some Proteins"/> |
| 62 <param name="count" value="3"/> | 85 <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> |
| 63 <param name="set" value="rhodopsin_proteins.fasta"/> | 86 <param name="sets_0|lab" value="Rhodopsins"/> |
| 64 <param name="lab" value="Rhodopsins"/> | 87 <param name="sets_1|set" value="four_human_proteins.fasta"/> |
| 65 <param name="set" value="four_human_proteins.fasta"/> | 88 <param name="sets_1|lab" value="Human"/> |
| 66 <param name="lab" value="Human"/> | 89 <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> |
| 67 <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/> | 90 <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> |
| 68 <param name="lab" value="Human vs Rhodopsin BLAST"/> | 91 <assert_stdout> |
| 69 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> | 92 <has_line line="Doing 3-way Venn Diagram" /> |
| 93 <has_line line="Total of 10 IDs" /> | |
| 94 </assert_stdout> | |
| 95 <assert_stderr> | |
| 96 <has_text_matching expression="Unexpected ID sp|Q9BS26|ERP44_HUMAN in fasta file *" /> | |
| 97 </assert_stderr> | |
| 70 </test> | 98 </test> |
| 71 --> | |
| 72 </tests> | 99 </tests> |
| 73 <help> | 100 <help> |
| 74 | 101 |
| 75 .. class:: infomark | 102 .. class:: infomark |
| 76 | 103 |