Mercurial > repos > iuc > pe_histogram

annotate pe_histogram.xml @ 5:551f36b118b1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit d7e29bd902ec805b3e8d68c38ae446ec25f9cb43
author iuc
date Fri, 04 Oct 2024 09:11:24 +0000
parents 784273cfcebc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
551f36b118b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit d7e29bd902ec805b3e8d68c38ae446ec25f9cb43
iuc
parents: 4
diff changeset
1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.2" profile="23.0">
0
638c1e914099 Uploaded
iuc
parents:
diff changeset
2 <description>of insert size frequency</description>
638c1e914099 Uploaded
iuc
parents:
diff changeset
3 <requirements>
4
784273cfcebc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents: 3
diff changeset
4 <requirement type="package" version="11.0.1">openjdk</requirement>
784273cfcebc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents: 3
diff changeset
5 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
0
638c1e914099 Uploaded
iuc
parents:
diff changeset
6 </requirements>
3
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
8 ln -s '${input_bam}' localbam.bam &&
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
9 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
10 java -jar '$__tool_directory__/PEHistogram.jar'
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
11 -B localbam.bam
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
12 -I localbam.bam.bai
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
13 #if str($lower_limit):
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
14 -l $lower_limit
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
15 #end if
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
16 #if str($upper_limit):
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
17 -u $upper_limit
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
18 #end if
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
19 -p '$output1'
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
20 -t '$output2'
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
21 1>/dev/null
99c86046c72a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
iuc
parents: 2
diff changeset
22 ]]></command>
0
638c1e914099 Uploaded
iuc
parents:
diff changeset
23 <inputs>
638c1e914099 Uploaded
iuc
parents:
diff changeset
24 <param name="input_bam" type="data" format="bam" label="BAM file" />
4
784273cfcebc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents: 3
diff changeset
25 <param name="lower_limit" type="integer" value="" optional="true" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
784273cfcebc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
iuc
parents: 3
diff changeset
26 <param name="upper_limit" type="integer" value="" optional="true" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
0
638c1e914099 Uploaded
iuc
parents:
diff changeset
27 </inputs>
638c1e914099 Uploaded
iuc
parents:
diff changeset
28 <outputs>
5
551f36b118b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit d7e29bd902ec805b3e8d68c38ae446ec25f9cb43
iuc
parents: 4
diff changeset
29 <data name="output1" format="png" label="${tool.name} on ${on_string}: Plot"/>
551f36b118b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit d7e29bd902ec805b3e8d68c38ae446ec25f9cb43
iuc
parents: 4
diff changeset
30 <data name="output2" format="tabular" label="${tool.name} on ${on_string}: Table" />
0
638c1e914099 Uploaded
iuc
parents:
diff changeset
31 </outputs>
638c1e914099 Uploaded
iuc
parents:
diff changeset
32 <tests>
638c1e914099 Uploaded
iuc
parents:
diff changeset
33 <test>
638c1e914099 Uploaded
iuc
parents:
diff changeset
34 <param name="input_bam" value="input.bam" ftype="bam" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
35 <output name="output1" file="output1.png" ftype="png" compare="sim_size" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
36 <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
37 </test>
638c1e914099 Uploaded
iuc
parents:
diff changeset
38 <test>
638c1e914099 Uploaded
iuc
parents:
diff changeset
39 <param name="input_bam" value="input.bam" ftype="bam" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
40 <param name="lower_limit" value="200" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
41 <param name="upper_limit" value="300" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
42 <output name="output1" file="output2.png" ftype="png" compare="sim_size" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
43 <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" />
638c1e914099 Uploaded
iuc
parents:
diff changeset
44 </test>
638c1e914099 Uploaded
iuc
parents:
diff changeset
45 </tests>
638c1e914099 Uploaded
iuc
parents:
diff changeset
46 <help>
638c1e914099 Uploaded
iuc
parents:
diff changeset
47
638c1e914099 Uploaded
iuc
parents:
diff changeset
48 **What it does**
638c1e914099 Uploaded
iuc
parents:
diff changeset
49
638c1e914099 Uploaded
iuc
parents:
diff changeset
50 Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced:
638c1e914099 Uploaded
iuc
parents:
diff changeset
51
638c1e914099 Uploaded
iuc
parents:
diff changeset
52 - a png image consisting of the histogram of the insert size frequency
638c1e914099 Uploaded
iuc
parents:
diff changeset
53 - a tabular file containing the alignment statistics
638c1e914099 Uploaded
iuc
parents:
diff changeset
54
638c1e914099 Uploaded
iuc
parents:
diff changeset
55 -----
638c1e914099 Uploaded
iuc
parents:
diff changeset
56
638c1e914099 Uploaded
iuc
parents:
diff changeset
57 **Options**
638c1e914099 Uploaded
iuc
parents:
diff changeset
58
638c1e914099 Uploaded
iuc
parents:
diff changeset
59 * **Lower bp limit** - the lower bp limit on insert size for calculating the histogram.
638c1e914099 Uploaded
iuc
parents:
diff changeset
60 * **Upper bp limit** - the upper bp limit on insert size for calculating the histogram.
638c1e914099 Uploaded
iuc
parents:
diff changeset
61
638c1e914099 Uploaded
iuc
parents:
diff changeset
62 </help>
638c1e914099 Uploaded
iuc
parents:
diff changeset
63 <citations>
638c1e914099 Uploaded
iuc
parents:
diff changeset
64 <citation type="bibtex">
638c1e914099 Uploaded
iuc
parents:
diff changeset
65 @unpublished{None,
638c1e914099 Uploaded
iuc
parents:
diff changeset
66 author = {Lai, William},
638c1e914099 Uploaded
iuc
parents:
diff changeset
67 title = {None},
638c1e914099 Uploaded
iuc
parents:
diff changeset
68 year = {None},
638c1e914099 Uploaded
iuc
parents:
diff changeset
69 eprint = {None},
638c1e914099 Uploaded
iuc
parents:
diff changeset
70 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
638c1e914099 Uploaded
iuc
parents:
diff changeset
71 }</citation>
638c1e914099 Uploaded
iuc
parents:
diff changeset
72 </citations>
638c1e914099 Uploaded
iuc
parents:
diff changeset
73 </tool>