Mercurial > repos > kyost > atac_primer_tool

comparison find_qPCR_regions.xml @ 0:fd3ea97a96bc draft

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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Sat, 28 Apr 2018 15:07:26 -0400
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1 <tool id="find_qPCR_regions" name="Find ATAC qPCR regions" version="0.1.0">
2 <description> Determines optimal regions for designing ATAC-qPCR primers.</description>
3 <requirements>
4 <requirement type="package" version="3.4.2" >r-base</requirement>
5 </requirements>
6 <command><![CDATA[
7 Rscript --vanilla $__tool_directory__/find_qPCR_regions.R $input1 $input2 $input3 $input4 $input5 $output
8 ]]></command>
9 <inputs>
10 <param type="data" name="input1" format="tabular" label="Coverage Bed File"/>
11 <param type="data" name="input2" format="tabular" label="Spanning Fragment Coverage Bed File"/>
12 <param type="data" name="input3" format="tabular" label="Total Read Counts"/>
13 <param type="float" name="input4" value="0.8" label="Correlation Cutoff"/>
14 <param type="integer" name="input5" value="3" label="Coverage Cutoff"/>
15 </inputs>
16 <outputs>
17 <data name="output" format="bed" />
18 </outputs>
19 <tests>
20 <test>
21 <param name="input1" value="combined.o.bed.coverage"/>
22 <param name="input2" value="combined.f9.bed.coverage"/>
23 <param name="input3" value="lib_sizes.txt"/>
24 <param name="input4" value="0.7"/>
25 <param name="input5" value="2"/>
26 <output name="output" file="qPCR_regions.bed"/>
27 </test>
28 </tests>
29 <help><![CDATA[
30 Determines optimal regions for designing ATAC-qPCR primers based on correlation between spanning fragments and total peak height.
31 ]]></help>
32 <citations>
33 <citation type="doi">doi:10.1038/nmeth.4663</citation>
34 </citations>
35 </tool>