Mercurial > repos > iuc > pe_histogram
comparison pe_histogram.xml @ 3:bd1416eea1f0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"
author | iuc |
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date | Wed, 04 Dec 2019 08:18:34 -0500 |
parents | 9be99db0304a |
children | 594b85e4237a |
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2:9be99db0304a | 3:bd1416eea1f0 |
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1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> | 1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> |
2 <description>of insert size frequency</description> | 2 <description>of insert size frequency</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="8.0.112">openjdk</requirement> | 4 <requirement type="package" version="11.0.1">openjdk</requirement> |
5 <requirement type="package" version="1">fonts-conda-ecosystem</requirement> | |
5 </requirements> | 6 </requirements> |
6 <command detect_errors="aggressive"><![CDATA[ | 7 <command detect_errors="aggressive"><![CDATA[ |
7 ln -s '${input_bam}' localbam.bam && | 8 ln -s '${input_bam}' localbam.bam && |
8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai && | 9 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai && |
9 java -jar '$__tool_directory__/PEHistogram.jar' | 10 java -jar '$__tool_directory__/PEHistogram.jar' |
19 -t '$output2' | 20 -t '$output2' |
20 1>/dev/null | 21 1>/dev/null |
21 ]]></command> | 22 ]]></command> |
22 <inputs> | 23 <inputs> |
23 <param name="input_bam" type="data" format="bam" label="BAM file" /> | 24 <param name="input_bam" type="data" format="bam" label="BAM file" /> |
24 <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."/> | 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."/> |
25 <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." /> | 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." /> |
26 </inputs> | 27 </inputs> |
27 <outputs> | 28 <outputs> |
28 <data name="output1" format="png" /> | 29 <data name="output1" format="png" /> |
29 <data name="output2" format="tabular" /> | 30 <data name="output2" format="tabular" /> |
30 </outputs> | 31 </outputs> |