annotate vvv2_display.xml @ 20:882318c1e5b7 draft default tip

Uploaded, try correct vcf output def with conditional input

<tool id="vvv2_display" name="vvv2_display: Display SNP proportions and CDS of an assembly in png image" version="0.2.5.0" python_template_version="3.9">
    <requirements>
      <requirement type="package" version="0.2.5.0">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' -N '$contig_names' $cov_depth_scale 
       ## vcf significant output file option
       #if str($option_snp_vcf_summary.boolean) == '2':
           -x '${option_snp_vcf_summary.snp_vcf_summary_f}'
       #end if
    ]]></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" />
        <conditional name="option_snp_vcf_summary">
          <param type="select" name="boolean" label="tells if vcf summary output file is created" help="tells if vcf summary output file is created">
            <option value="1">no summary vcf output</option>
		  	    <option value="2">additional vcf summary output</option>
          </param>
          <when value="2">
            <param type="data" name="snp_vcf_summary" format="vcf" argument="-x" help="provide the vcf summary output file name"/>
                <expand macro="snp_vcf_summary_f"/>
            </param>
          </when>
        </conditional>  
    </inputs>
    <outputs>
        <data name="snp_img" format="png" label="png image showing variants"/>
        <data name="snp_loc_summary" format="tabular" label="tsv file of significant variants only"/>
        <!-- present only if ask for summary vcf output-->
        <data name="option_snp_vcf_summary|snp_vcf_summary" format="vcf" label="vcf file of significant variants only" optional="true">
          <filter>option_snp_vcf_summary['boolean'] == "1"</filter>
        </data>
	<!-- intermediate output files added for Galaxy compatibility -->
        <data name="snp_loc" format="txt" hidden="true" label="tsv file of all variants"/>
        <data name="json_annot" format="json" hidden="true" label="json file of annotations"/>
        <data name="bed_annot" format="bed" hidden="true" label="bed file of of annotations"/>
        <data name="correct_vcf" format="vcf" hidden="true" label="vcf file of variants corrected for positions when multi contigs"/>
        <data name="contig_limits" format="txt" hidden="true" label="txt file with contig limits"/>
        <data name="contig_names" format="txt" hidden="true" label="txt file with contig names"/>
        <data name="cov_depth_corr" format="txt" hidden="true" label="txt file with pos and cov depth, pos corrected when multi contigs"/>
	<!-- end intermediate output files added for Galaxy compatibility -->		
    </outputs>
    <tests>
      <test>
            <param name="vadr_fail_annotation" value="test_vvv2_display/res_vadr_fail.tbl" ftype="tabular"/>	
            <param name="vadr_pass_annotation" value="test_vvv2_display/res_vadr_pass.tbl" ftype="tabular"/>
            <param name="vadr_seqstat" value="test_vvv2_display/res_vadr.seqstat" ftype="txt"/>
            <param name="vardict_vcf" value="test_vvv2_display/res_vardict.vcf" ftype="vcf"/>
            <param name="var_significant_thres" value="7"/>
            <param name="cov_depth_scale" value="-y" />
            <param name="cov_depth" value="test_vvv2_display/res_covdepth.txt" />
            <param name="option_snp_vcf_summary|boolean" value="2">
            <output name="snp_img" file="test_vvv2_display/res_snp.png" ftype="png"/>	    
            <output name="snp_loc_summary" file="test_vvv2_display/res_snp_summary.tsv" ftype="tabular"/>
            <output name="option_snp_vcf_summary|snp_vcf_summary" file="test_vvv2_display/res_snp_summary.vcf" ftype="vcf"/>
	          <!-- intermediate output files -->
            <output name="snp_loc" file="test_vvv2_display/res_snp.txt" ftype="txt"/>
	          <output name="json_annot" file="test_vvv2_display/res_vadr.json" ftype="json"/>
            <output name="bed_annot" file="test_vvv2_display/res_vadr.4vardict.bed" ftype="bed"/>
            <output name="correct_vcf" file="test_vvv2_display/res_correct.vcf" ftype="vcf"/>
            <output name="contig_limits" file="test_vvv2_display/contig_limits.txt" ftype="txt"/>
            <output name="contig_names" file="test_vvv2_display/contig_names.txt" ftype="txt"/>
            <output name="cov_depth_corr" file="test_vvv2_display/res_covdepth_corrected.txt" ftype="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>