Mercurial > repos > tiagoantao > clone_filter
comparison STACKS_clone_filter.xml @ 0:42e64fbf4609 draft
planemo upload commit 60a090d1dc89c2eb383feeb35cd6078b9130e0e5-dirty
author | tiagoantao |
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date | Tue, 02 Feb 2016 21:15:50 -0500 |
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children | b91ab894f6e0 |
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1 <tool id="STACKS_clone_filter" name="STACKS: clone_filter" version="0.9.0"> | |
2 <description>Run the STACKS clone_filter program</description> | |
3 | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="1.18">stacks</requirement> | |
7 </requirements> | |
8 | |
9 <stdio> | |
10 <exit_code range="1" level="fatal" description="Error in Stacks clone_filter" /> | |
11 </stdio> | |
12 | |
13 <command interpreter="python"> | |
14 STACKS_clone_filter.py | |
15 #if $data_type.dt_select == 'single': | |
16 -f $data_type.fname | |
17 #else | |
18 -1 $data_type.fwd | |
19 -2 $data_type.rev | |
20 #end if | |
21 </command> | |
22 | |
23 <inputs> | |
24 <conditional name="data_type"> | |
25 <param name="dt_select" type="select" label="Single or Paired-end"> | |
26 <option value="single">Single</option> | |
27 <option value="pair">Pair</option> | |
28 </param> | |
29 <when value="single"> | |
30 <param name="fname" type="fastq" label="FASTQ" /> | |
31 </when> | |
32 <when value="pair"> | |
33 <param name="fwd" type="fastq" label="Forward FASTQ" /> | |
34 <param name="rev" type="fastq" label="Reverse FASTQ" /> | |
35 </when> | |
36 </conditional> | |
37 </inputs> | |
38 | |
39 <outputs> | |
40 <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq"> | |
41 <filter>data_type['dt_select'] == 'single' </filter> | |
42 </data> | |
43 <data format="fastq" name="clean_fwd" from_work_dir="job_outputs/fwd.fq"> | |
44 <filter>data_type['dt_select'] == 'pair' </filter> | |
45 </data> | |
46 <data format="fastq" name="clean_rev" from_work_dir="job_outputs/rev.fq"> | |
47 <filter>data_type['dt_select'] == 'pair' </filter> | |
48 </data> | |
49 </outputs> | |
50 | |
51 <tests> | |
52 <test> | |
53 <param name="dt_select" value="pair" /> | |
54 <param name="fwd" value="fwd.fq" /> | |
55 <param name="rev" value="rev.fq" /> | |
56 <output name="clean_fwd" /> | |
57 <output name="clean_rev" /> | |
58 </test> | |
59 </tests> | |
60 | |
61 <help> | |
62 -------- | |
63 | |
64 **Project links:** | |
65 | |
66 `STACKS website <http://creskolab.uoregon.edu/stacks/>`_ . | |
67 | |
68 `STACKS manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ . | |
69 | |
70 `STACKS google group <https://groups.google.com/forum/#!forum/stacks-users>`_ . | |
71 | |
72 </help> | |
73 <citations> | |
74 <citation type="doi">10.1111/mec.12354</citation> | |
75 <citation type="doi">10.1111/mec.12330</citation> | |
76 <citation type="doi">10.1534/g3.111.000240</citation> | |
77 <citation type="doi">10.1534/genetics.111.127324</citation> | |
78 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> | |
79 <citation type="doi">10.1073/pnas.1006538107</citation> | |
80 </citations> | |
81 </tool> |