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vvv2_display.xml
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<tool id="vvv2_display" name="vvv2_display: Display SNP proportions and CDS of an assembly in png image" version="0.2.3.5" python_template_version="3.9">
<requirements>
<requirement type="package" version="0.2.3.5">vvv2_display</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
vvv2_display.py -f '$vadr_fail_annotation' -p '$vadr_pass_annotation' -s '$vadr_seqstat' -n '$vardict_vcf' -r '$snp_img' -w '$var_significant_thres' -o '$cov_depth' -e '$cov_depth_corr' -t '$snp_loc' -u '$snp_loc_summary' -j '$json_annot' -k '$bed_annot' -l '$correct_vcf' -m '$contig_limits' $cov_depth_scale
]]></command>
<inputs>
<param type="data" name="vadr_fail_annotation" format="tabular" />
<param type="data" name="vadr_pass_annotation" format="tabular" />
<param type="data" name="vadr_seqstat" format="txt" />
<param type="data" name="vardict_vcf" format="vcf" />
<param type="integer" name="var_significant_thres" value="7" min="0" max="100" label="min int threshold to keep significant variant (%age)" format="int" />
<param type="select" name="cov_depth_scale" label="tells if cov depth scale (ordinate) is displayed with log10 (default) or linear scale" help="tells if cov depth scale (ordinate) is displayed with log10 (default) or linear scale">
<option value="">log10 scale</option>
<option value="-y">linear scale</option>
</param>
<param type="data" name="cov_depth" format="txt" />
</inputs>
<outputs>
<data name="snp_img" format="png" />
<data name="snp_loc_summary" format="txt" />
<!-- intermediate output files added for Galaxy compatibility -->
<data name="snp_loc" format="txt" />
<data name="json_annot" format="json" />
<data name="bed_annot" format="bed" />
<data name="correct_vcf" format="vcf" />
<data name="contig_limits" format="txt" />
<!-- end intermediate output files added for Galaxy compatibility -->
<data name="cov_depth_corr" format="txt" />
</outputs>
<tests>
<test>
<param name="vadr_fail_annotation" value="test_vvv2_display/res_vadr_fail.tbl"/>
<param name="vadr_pass_annotation" value="test_vvv2_display/res_vadr_pass.tbl"/>
<param name="vadr_seqstat" value="test_vvv2_display/res_vadr.seqstat"/>
<param name="vardict_vcf" value="test_vvv2_display/res_vardict.vcf"/>
<param name="var_significant_thres" value="7"/>
<param name="cov_depth_scale" value="test_vvv2_display/res_covdepth.txt" />
<output name="snp_img" file="test_vvv2_display/res_snp.png"/>
<output name="snp_loc_summary" file="test_vvv2_display/res_snp_summary.txt"/>
<!-- intermediate output files -->
<output name="snp_loc" file="test_vvv2_display/res_snp.txt"/>
<output name="json_annot" file="test_vvv2_display/res_vadr.json"/>
<output name="bed_annot" file="test_vvv2_display/res_vadr.4vardict.bed"/>
<output name="correct_vcf" file="test_vvv2_display/res_correct.vcf"/>
<output name="contig_limits" file="test_vvv2_display/contig_limits.txt"/>
<output name="cov_depth_corr" file="test_vvv2_display/res_covdepth_corrected.txt"/>
<!-- end intermediate output files -->
</test>
</tests>
<help><![CDATA[
[vvv2_display.py]
Aim: Display of SNP proportions, annotations, for an assembly
in:
- vardict variant calling output
- vadr assembly annotations
out:
- png file (image of SNP proportion alongside the assembly with CDS positions)
- txt file with variant calling summary, location in CDS and surround DNA sequence.
usage: vvv2_display.py [-h] [-p FILE] [-f FILE] [-s FILE] [-n FILE] [-r FILE]
optional arguments:
-h, --help show this help message and exit
-p FILE, --pass_tbl_f FILE
in: tabular file of vadr annotations, with pass status
-f FILE, --fail_tbl_f FILE
in: tabular file of vadr annotations, with fail status
-s FILE, --seq_stat_f FILE
in: seq stat file of vadr annotator
-n FILE, --vcf_f FILE
in: vcf variant file provided by vardict
-r FILE, --png_var_f FILE
out: png file with variant proportions and annotations
-o FILE, --cov_depth_f FILE
[optional] in: text file of coverage depths (given by samtools depth)
]]></help>
<citations>
<citation type="bibtex">
@misc{githubvvv2_display,
author = {Touzain, Fabrice},
year = {2022},
title = {vvv2_display},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/ANSES-Ploufragan/vvv2_display},
}</citation>
<citation type="doi">10.1016/j.virusres.2020.198201</citation>
</citations>
</tool>