Mercurial > repos > nml > quasitools
annotate callntvar.xml @ 5:b69e898b8109 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
author | nml |
---|---|
date | Fri, 24 Aug 2018 16:50:28 -0400 |
parents | 8cdffc02d2e2 |
children | dcd43b402eb3 |
rev | line source |
---|---|
5
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
4
diff
changeset
|
1 <tool id="callntvar" name="Nucleotide Variants" version="0.4.2"> |
0
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
2 <description>Identifies nucleotide variants</description> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
3 <requirements> |
5
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
4
diff
changeset
|
4 <requirement type="package" version="0.4.2">quasitools</requirement> |
0
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
5 </requirements> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
6 <command detect_errors="exit_code"><![CDATA[ |
5
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
4
diff
changeset
|
7 |
0
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && |
5
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
4
diff
changeset
|
9 quasitools call ntvar $input_bam $ref_file |
0
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
10 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
11 #if $error_rate: |
5
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
4
diff
changeset
|
12 -e $error_rate |
0
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
13 #end if |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
14 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
15 -o output.vcf |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
16 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
17 ]]></command> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
18 <inputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
19 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
20 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
21 <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.01" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.01."/> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
22 </inputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
23 <outputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
24 <data format="vcf" name="output" from_work_dir="output.vcf" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
25 </outputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
26 <tests> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
27 <test> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
28 <param name="input_bam" value="align.bam" ftype="bam" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
29 <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
30 <output name="output" > |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
31 <assert_contents> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
32 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
33 <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s69\sPASS\sDP=157;AC=12;AF=0.0764" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
34 </assert_contents> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
35 </output> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
36 </test> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
37 </tests> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
38 <help><![CDATA[ |
5
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
4
diff
changeset
|
39 |
0
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
40 Nucleotide Variants |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
41 =================== |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
42 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
43 Call nucleotide variants for a given BAM file and a supplied reference file. |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
44 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
45 ]]></help> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
46 <citations> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
47 </citations> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
diff
changeset
|
48 </tool> |