Mercurial > repos > peterjc > venn_list

comparison tools/plotting/venn_list.xml @ 4:29fcd027d67a draft

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Uploaded v0.0.6 take 1, simple test (which currently fails)
author peterjc
date Thu, 16 May 2013 12:43:57 -0400
parents aefc86eda5f6
children 6ebfb498c2c4
comparison
equal deleted inserted replaced
3:bacb7dfa846c 4:29fcd027d67a
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"/>