Mercurial > repos > nml > quasitools

annotate callaavar.xml @ 0:1f1214983a1c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:05:57 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
1 <tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
2 <description>Identifies amino acid mutations</description>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
3 <macros>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
4 <import>macros.xml</import>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
5 </macros>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
6 <expand macro="requirements"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
8
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
9 ln -s $input_bam '${input_bam.name}' &&
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
11
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
12 quasitools call aavar '${input_bam.name}' $ref_file $input_genes
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
13
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
14 #if $var_file:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
15 $var_file
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
16 #end if
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
17
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
18 #if $mutation_db:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
19 $mutation_db
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
20 #end if
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
21
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
22 #if $min_freq:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
23 -f $min_freq
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
24 #end if
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
25
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
26 #if $error_rate:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
27 -e $error_rate
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
28 #end if
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
29
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
30 -o output.vcf
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
31
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
32 ]]></command>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
33 <inputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
34 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
35 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
36 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
37 <param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
38 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
39 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
40 <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
41 </inputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
42 <outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
43 <data format="vcf" name="output" from_work_dir="output.vcf" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
44 </outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
45 <tests>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
46 <test>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
47 <param name="input_bam" value="align.bam" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
48 <param name="ref_file" value="hxb2_pol.fas" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
49 <param name="var_file" value="nt_variants.vcf" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
50 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
51 <param name="min_freq" value="0.01" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
52 <output name="output" >
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
53 <assert_contents>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
54 <has_text_matching expression="#CHROM"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
55 <has_text_matching expression="0.0779" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
56 <has_text_matching expression="0.0103;CAT=.;SRVL=." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
57 <has_text_matching expression="0.0163;CAT=.;SRVL=." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
58 <has_text_matching expression="0.0148;CAT=.;SRVL=." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
59 <has_text_matching expression="0.0234;CAT=.;SRVL=." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
60 <has_text_matching expression="0.0159;CAT=.;SRVL=." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
61 </assert_contents>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
62 </output>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
63 </test>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
64 </tests>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
65 <help><![CDATA[
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
66
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
67 Amino Acid Variants
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
68 ===================
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
69
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
70 Identifies amino acid mutations for a BAM file.
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
71
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
72
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
73
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
74 ]]></help>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
75 <expand macro="citations" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
76 </tool>