annotate 4_merge_sites.xml @ 46:d273453b30bb
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
| author |
jpayne |
| date |
Tue, 07 May 2019 16:01:52 -0400 |
| parents |
f58616a4b2f3 |
| children |
1667e4c08344 |
| rev |
line source |
|
jpayne@0
|
1 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
|
|
jpayne@0
|
2 <description>from multiple samples</description>
|
|
jpayne@0
|
3 <requirements>
|
|
jpayne@0
|
4 <requirement type="package" version="2.2.6">bowtie2</requirement>
|
|
jpayne@0
|
5 <requirement type="package" version="1.2">samtools</requirement>
|
|
jpayne@12
|
6 <requirement type="package" version="1.0.6">bzip2</requirement>
|
|
jpayne@35
|
7 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
|
|
jpayne@46
|
8 <requirement type="package" version="3.6.0">python</requirement>
|
|
jpayne@0
|
9 </requirements>
|
|
jpayne@0
|
10 <command detect_errors="exit_code"><![CDATA[
|
|
jpayne@40
|
11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
|
|
jpayne@45
|
12 # env &&
|
|
jpayne@9
|
13 python $__tool_directory__/snp-wind.py ./
|
|
jpayne@0
|
14 #for $call in $calls
|
|
jpayne@0
|
15 -n $call.element_identifier -f $call
|
|
jpayne@0
|
16 #end for
|
|
jpayne@0
|
17 -p "var.fit.vcf" > ./file
|
|
jpayne@0
|
18 && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist
|
|
jpayne@0
|
19 ]]></command>
|
|
jpayne@0
|
20 <inputs>
|
|
jpayne@0
|
21 <param type="data_collection" name="calls" format="vcf" collection_type="list" />
|
|
jpayne@0
|
22 </inputs>
|
|
jpayne@0
|
23 <outputs>
|
|
jpayne@0
|
24 <data name="snplist" format="txt" />
|
|
jpayne@0
|
25 </outputs>
|
|
jpayne@0
|
26 <tests>
|
|
jpayne@0
|
27 <test>
|
|
jpayne@0
|
28 <param name="calls">
|
|
jpayne@0
|
29 <collection type="list">
|
|
jpayne@39
|
30 <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" ftype="fastqsanger" />
|
|
jpayne@39
|
31 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" />
|
|
jpayne@39
|
32 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" />
|
|
jpayne@39
|
33 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" />
|
|
jpayne@0
|
34 </collection>
|
|
jpayne@0
|
35 </param>
|
|
jpayne@0
|
36 <!-- <output name="snplist" value="snplist.txt" /> -->
|
|
jpayne@0
|
37 </test>
|
|
jpayne@0
|
38 </tests>
|
|
jpayne@0
|
39 <help><![CDATA[
|
|
jpayne@0
|
40 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
|
|
jpayne@0
|
41 ]]></help>
|
|
jpayne@0
|
42 <citations>
|
|
jpayne@0
|
43 <citation type="doi">10.7717/peerj-cs.20</citation>
|
|
jpayne@0
|
44 </citations>
|
|
jpayne@0
|
45 </tool> |
