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