Mercurial > repos > peterjc > venn_list
comparison tools/plotting/venn_list.xml @ 4:29fcd027d67a draft
Uploaded v0.0.6 take 1, simple test (which currently fails)
author | peterjc |
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date | Thu, 16 May 2013 12:43:57 -0400 |
parents | aefc86eda5f6 |
children | 6ebfb498c2c4 |
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3:bacb7dfa846c | 4:29fcd027d67a |
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1 <tool id="venn_list" name="Venn Diagram" version="0.0.3"> | 1 <tool id="venn_list" name="Venn Diagram" version="0.0.6"> |
2 <description>from lists</description> | 2 <description>from lists</description> |
3 <requirements> | |
4 <requirement type="python-module">rpy</requirement> | |
5 <requirement type="python-module">Bio</requirement> | |
6 </requirements> | |
3 <command interpreter="python"> | 7 <command interpreter="python"> |
4 venn_list.py | 8 venn_list.py |
5 #if $universe.type_select=="implicit": | 9 #if $universe.type_select=="implicit": |
6 - - | 10 - - |
7 #else: | 11 #else: |
10 "$main_lab" | 14 "$main_lab" |
11 #for $s in $sets: | 15 #for $s in $sets: |
12 $s.set $s.set.ext "$s.lab" | 16 $s.set $s.set.ext "$s.lab" |
13 #end for | 17 #end for |
14 $PDF</command> | 18 $PDF</command> |
19 <stdio> | |
20 <!-- Anything other than zero is an error --> | |
21 <exit_code range="1:" /> | |
22 <exit_code range=":-1" /> | |
23 </stdio> | |
15 <inputs> | 24 <inputs> |
16 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> | 25 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> |
17 <conditional name="universe"> | 26 <conditional name="universe"> |
18 <param name="type_select" type="select" label="Implicit or explicit full ID list?"> | 27 <param name="type_select" type="select" label="Implicit or explicit full ID list?"> |
19 <option value="explicit">Explicit</option> | 28 <option value="explicit">Explicit</option> |
30 </repeat> | 39 </repeat> |
31 </inputs> | 40 </inputs> |
32 <outputs> | 41 <outputs> |
33 <data format="pdf" name="PDF" /> | 42 <data format="pdf" name="PDF" /> |
34 </outputs> | 43 </outputs> |
35 <requirements> | |
36 <requirement type="python-module">rpy</requirement> | |
37 <requirement type="python-module">Bio</requirement> | |
38 </requirements> | |
39 <tests> | 44 <tests> |
40 <!-- Doesn't seem to work properly, manages to get two sets, both | 45 <!-- Doesn't seem to work properly, manages to get two sets, both |
41 with same FASTA file, but second with default "Group" label. | 46 with same FASTA file, but second with default "Group" label. --> |
42 <test> | 47 <test> |
43 <param name="type_select" value="explicit"/> | 48 <param name="type_select" value="explicit"/> |
44 <param name="main" value="venn_list.tabular" ftype="tabular"/> | 49 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
45 <param name="main_lab" value="Some Proteins"/> | 50 <param name="main_lab" value="Some Proteins"/> |
46 <param name="set" value="rhodopsin_proteins.fasta"/> | 51 <param name="set" value="rhodopsin_proteins.fasta"/> |
47 <param name="lab" value="Rhodopsins"/> | 52 <param name="lab" value="Rhodopsins"/> |
48 <output name="PDF" file="venn_list1.pdf" ftype="pdf"/> | 53 <output name="PDF" file="venn_list1.pdf" ftype="pdf"/> |
49 </test> | 54 </test> |
50 --> | |
51 <!-- Can't use more than one repeat value in tests (yet) | 55 <!-- Can't use more than one repeat value in tests (yet) |
52 <test> | 56 <test> |
53 <param name="type_select" value="explicit"/> | 57 <param name="type_select" value="explicit"/> |
54 <param name="main" value="venn_list.tabular" ftype="tabular"/> | 58 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
55 <param name="main_lab" value="Some Proteins"/> | 59 <param name="main_lab" value="Some Proteins"/> |