Mercurial > repos > iuc > pe_histogram
annotate pe_histogram.xml @ 2:d23480305b5a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
| author | iuc |
|---|---|
| date | Fri, 13 Jan 2017 10:33:31 -0500 |
| parents | 638c1e914099 |
| children | 99c86046c72a |
| rev | line source |
|---|---|
|
2
d23480305b5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
iuc
parents:
0
diff
changeset
|
1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> |
| 0 | 2 <description>of insert size frequency</description> |
| 3 <requirements> | |
|
2
d23480305b5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 37b1832f15c9960e02c6cae831b1f9f717818af8
iuc
parents:
0
diff
changeset
|
4 <requirement type="package" version="8.0.112">openjdk</requirement> |
| 0 | 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> |