Mercurial > repos > kyost > atac_primer_tool
annotate find_qPCR_regions.xml @ 0:fd3ea97a96bc draft
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author | kyost |
---|---|
date | Sat, 28 Apr 2018 15:07:26 -0400 |
parents | |
children |
rev | line source |
---|---|
0
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
1 <tool id="find_qPCR_regions" name="Find ATAC qPCR regions" version="0.1.0"> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
2 <description> Determines optimal regions for designing ATAC-qPCR primers.</description> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
3 <requirements> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
4 <requirement type="package" version="3.4.2" >r-base</requirement> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
5 </requirements> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
6 <command><![CDATA[ |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
7 Rscript --vanilla $__tool_directory__/find_qPCR_regions.R $input1 $input2 $input3 $input4 $input5 $output |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
8 ]]></command> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
9 <inputs> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
10 <param type="data" name="input1" format="tabular" label="Coverage Bed File"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
11 <param type="data" name="input2" format="tabular" label="Spanning Fragment Coverage Bed File"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
12 <param type="data" name="input3" format="tabular" label="Total Read Counts"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
13 <param type="float" name="input4" value="0.8" label="Correlation Cutoff"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
14 <param type="integer" name="input5" value="3" label="Coverage Cutoff"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
15 </inputs> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
16 <outputs> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
17 <data name="output" format="bed" /> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
18 </outputs> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
19 <tests> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
20 <test> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
21 <param name="input1" value="combined.o.bed.coverage"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
22 <param name="input2" value="combined.f9.bed.coverage"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
23 <param name="input3" value="lib_sizes.txt"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
24 <param name="input4" value="0.7"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
25 <param name="input5" value="2"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
26 <output name="output" file="qPCR_regions.bed"/> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
27 </test> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
28 </tests> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
29 <help><![CDATA[ |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
30 Determines optimal regions for designing ATAC-qPCR primers based on correlation between spanning fragments and total peak height. |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
31 ]]></help> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
32 <citations> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
33 <citation type="doi">doi:10.1038/nmeth.4663</citation> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
34 </citations> |
fd3ea97a96bc
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff
changeset
|
35 </tool> |