Mercurial > repos > iuc > pe_histogram
comparison pe_histogram.xml @ 0:2f6c7f82ad4a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
author | iuc |
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date | Mon, 20 Jun 2016 13:02:17 -0400 |
parents | |
children | b1a427b17e9c |
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1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.0"> | |
2 <description>of insert size frequency</description> | |
3 <requirements> | |
4 <requirement type="package" version="8.0.45">java-jdk</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <!-- Anything other than zero is an error --> | |
8 <exit_code range=":-1" /> | |
9 <exit_code range="1:" /> | |
10 <!-- Check stderr in case the return code has not been set --> | |
11 <regex match="Error:" /> | |
12 <regex match="Exception:" /> | |
13 </stdio> | |
14 <command> | |
15 <![CDATA[ | |
16 ln -s "${input_bam}" "localbam.bam" && | |
17 ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" && | |
18 java -jar $__tool_directory__/PEHistogram.jar | |
19 -B "localbam.bam" | |
20 -I "localbam.bam.bai" | |
21 #if str($lower_limit) != '': | |
22 -l $lower_limit | |
23 #end if | |
24 #if str($upper_limit) != '': | |
25 -u $upper_limit | |
26 #end if | |
27 -p "$output1" | |
28 -t "$output2" 1>/dev/null | |
29 ]]> | |
30 </command> | |
31 <inputs> | |
32 <param name="input_bam" type="data" format="bam" label="BAM file" /> | |
33 <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/> | |
34 <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." /> | |
35 </inputs> | |
36 <outputs> | |
37 <data name="output1" format="png" /> | |
38 <data name="output2" format="tabular" /> | |
39 </outputs> | |
40 <tests> | |
41 <test> | |
42 <param name="input_bam" value="input.bam" ftype="bam" /> | |
43 <output name="output1" file="output1.png" ftype="png" compare="sim_size" /> | |
44 <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" /> | |
45 </test> | |
46 <test> | |
47 <param name="input_bam" value="input.bam" ftype="bam" /> | |
48 <param name="lower_limit" value="200" /> | |
49 <param name="upper_limit" value="300" /> | |
50 <output name="output1" file="output2.png" ftype="png" compare="sim_size" /> | |
51 <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" /> | |
52 </test> | |
53 </tests> | |
54 <help> | |
55 | |
56 **What it does** | |
57 | |
58 Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced: | |
59 | |
60 - a png image consisting of the histogram of the insert size frequency | |
61 - a tabular file containing the alignment statistics | |
62 | |
63 ----- | |
64 | |
65 **Options** | |
66 | |
67 * **Lower bp limit** - the lower bp limit on insert size for calculating the histogram. | |
68 * **Upper bp limit** - the upper bp limit on insert size for calculating the histogram. | |
69 | |
70 </help> | |
71 <citations> | |
72 <citation type="bibtex"> | |
73 @unpublished{None, | |
74 author = {Lai, William}, | |
75 title = {None}, | |
76 year = {None}, | |
77 eprint = {None}, | |
78 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} | |
79 }</citation> | |
80 </citations> | |
81 </tool> |