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comparison callntvar.xml @ 7:dcd43b402eb3 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author nml
date Fri, 23 Nov 2018 15:43:16 -0500
parents b69e898b8109
children 9def47f3c1e4
comparison
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6:9fb9fed71486 7:dcd43b402eb3
1 <tool id="callntvar" name="Nucleotide Variants" version="0.4.2"> 1 <tool id="callntvar" name="Nucleotide Variants" version="0.5.1">
2 <description>Identifies nucleotide variants</description> 2 <description>Identifies nucleotide variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.4.2">quasitools</requirement> 4 <requirement type="package" version="0.5.1">quasitools</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9 quasitools call ntvar $input_bam $ref_file 9 quasitools call ntvar $input_bam $ref_file
16 16
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> 19 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
20 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> 20 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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."/> 21 <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."/>
22 </inputs> 22 </inputs>
23 <outputs> 23 <outputs>
24 <data format="vcf" name="output" from_work_dir="output.vcf" /> 24 <data format="vcf" name="output" from_work_dir="output.vcf" />
25 </outputs> 25 </outputs>
26 <tests> 26 <tests>
28 <param name="input_bam" value="align.bam" ftype="bam" /> 28 <param name="input_bam" value="align.bam" ftype="bam" />
29 <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" /> 29 <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" />
30 <output name="output" > 30 <output name="output" >
31 <assert_contents> 31 <assert_contents>
32 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> 32 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
33 <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s69\sPASS\sDP=157;AC=12;AF=0.0764" /> 33 <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" />
34 <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" />
35 <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" />
34 </assert_contents> 36 </assert_contents>
35 </output> 37 </output>
36 </test> 38 </test>
37 </tests> 39 </tests>
38 <help><![CDATA[ 40 <help><![CDATA[
42 44
43 Call nucleotide variants for a given BAM file and a supplied reference file. 45 Call nucleotide variants for a given BAM file and a supplied reference file.
44 46
45 ]]></help> 47 ]]></help>
46 <citations> 48 <citations>
49 <citation type="bibtex">
50 @misc{GitHubquasitoolscallntvar,
51 title = {quasitools callntvar},
52 publisher = {phac-nml},
53 journal = {GitHub repository},
54 url = {https://github.com/phac-nml/quasitools},
55 }
56 </citation>
47 </citations> 57 </citations>
48 </tool> 58 </tool>