galaxy_cheripic_tool.xml in cheripic-1.2.5 vs galaxy_cheripic_tool.xml in cheripic-1.2.6

- old
+ new

@@ -1,23 +1,27 @@ -<tool id="cheripic" name="CHERIPIC" version="1.2.0"> +<tool id="cheripic" name="CHERIPIC" version="1.2.6"> <description>CHERIPIC</description> - <version_command>cheripic -v</version_command> + <version_command>/full_path_to/cheripic -v</version_command> <command> <![CDATA[ - cheripic + /full_path_to/cheripic --assembly $assembly + --input-format $input_format --mut-bulk $mut_bulk --bg-bulk $bg_bulk - --output $output + --mut-bulk-vcf $mut_bulk_vcf + --bg-bulk-vcf $bg_bulk_vcf --loglevel $loglevel --hmes-adjust $hmes_adjust --htlow $ht_low --hthigh $ht_high --mindepth $min_depth + --max-d-multiple $max_d_multiple + --maxdepth $max_depth --min-non-ref-count $min_non_ref_count --min-indel-count-support $min_indel_count_support --ambiguous-ref-bases $ambiguous_ref_bases --mapping-quality $mapping_quality --base-quality $base_quality @@ -26,21 +30,30 @@ --use-all-contigs $use_all_contigs --include-low-hmes $include_low_hmes --polyploidy $polyploidy --mut-parent $mut_parent --bg-parent $bg_parent + --repeats-file $repeats_file --bfr-adjust $bfr_adjust --sel-seq-len $sel_seq_len + &> output_log.txt ]]> </command> <inputs> <param name="assembly" type="data" format="fasta" label="Input Assembly file" help="Select Assembly fasta file" /> - <param name="mut_bulk" type="data" format="pileup" label="mutant bulk pileup file" help="Select mutant bulk pileup file" /> - <param name="bg_bulk" type="data" format="pileup" label="background bulk pileup file" min="1" multiple="true" help="Select background bulk pileup file" /> - <param name="loglevel" type="select" optional="true" label="analysis log level" help="choose between info, warn and debug levels"> - <option value="info" selected="true">info </option> + <param name="input_format" type="select" optional="true" label="input file format" help="choose between vcf, bam and pileup format" > + <option value="vcf" selected="true">vcf</option> + <option value="bam">bam</option> + <option value="pileup">pileup</option> + </param> + <param name="mut_bulk" type="data" label="mutant bulk input file" help="Select mutant bulk input file" /> + <param name="bg_bulk" type="data" label="background bulk input file" help="Select background bulk input file" /> + <param name="mut_bulk_vcf" type="data" optional="true" label="mutant bulk input vcf file" help="Select mutant bulk input vcf file" /> + <param name="bg_bulk_vcf" type="data" optional="true" label="background bulk input vcf file" help="Select background bulk input vcf file" /> + <param name="loglevel" type="select" optional="true" label="analysis log level" help="choose between info, warn and debug levels" > + <option value="info" selected="true">info</option> <option value="warn">warnings</option> <option value="debug">debug</option> </param> <param name="hmes_adjust" size="4" type="float" optional="true" value="0.5" min="0.01" max="1.0" label="hme score adjuster" help="factor added to snp count of each contig to adjust for hme score calculations" /> @@ -48,10 +61,14 @@ label="heterozygosity low limit" help="lower limit to heterozygosity allele fraction" /> <param name="ht_high" size="4" type="float" optional="true" value="0.75" min="0.1" max="1.0" label="heterozygosity high limit" help="upper limit to heterozygosity allele fraction" /> <param name="min_depth" size="4" type="integer" optional="true" value="6" min="1" max="8000" label="minimum read coverage" help="minimum read depth to conisder a position for variant calls" /> + <param name="max_d_multiple" size="4" type="integer" optional="true" value="5" min="0" max="100" + label="multiplication factor avg read coverage" help="multiplication factor for average coverage to calculate maximum read coverage" /> + <param name="max_depth" size="4" type="integer" optional="true" value="0" min="0" max="8000" + label="maximum read coverage" help="maximum read depth to conisder a position for variant calls" /> <param name="min_non_ref_count" size="4" type="integer" optional="true" value="3" min="1" max="8000" label="minimum alternate read coverage" help="minimum read depth supporting non reference base at each position" /> <param name="min_indel_count_support" size="4" type="integer" optional="true" value="3" min="1" max="8000" label="minimum indel read coverage" help="minimum read depth supporting an indel at each position" /> <param name="ambiguous_ref_bases" type="boolean" optional="true" checked="false" label="ambiguous reference position" @@ -71,24 +88,26 @@ help="option to select all contigs or only contigs containing variants for analysis" truevalue="true" falsevalue="false" /> <param name="include_low_hmes" type="boolean" optional="true" checked="false" label="no hme or bfr score cut off" help="option to include or discard variants from contigs with low hme-score or bfr score to list in the final output" truevalue="true" falsevalue="false" /> <param name="polyploidy" type="boolean" optional="true" checked="false" label="polyploid data" help="Set if the input data is from polyploids" truevalue="true" falsevalue="false" /> - <param name="mut-parent" type="data" optional="true" format="pileup" label="mutant parent pileup file" help="Select mutant parent pileup file" /> - <param name="bg-parent" type="data" optional="true" format="pileup" label="background parent pileup file" help="Select background parent pileup file" /> + <param name="mut_parent" type="data" optional="true" format="pileup" label="mutant parent pileup file" help="Select mutant parent pileup file" /> + <param name="bg_parent" type="data" optional="true" format="pileup" label="background parent pileup file" help="Select background parent pileup file" /> + <param name="repeats_file" type="data" optional="true" format="txt" label="Repeat masker output file" help="Repeat masker output file of repeat positions" /> <param name="bfr_adjust" size="4" type="float" optional="true" value="0.05" min="0.01" max="1.0" label="bfr score adjuster" help="factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05)" /> <param name="sel_seq_len" size="4" type="integer" optional="true" value="50" min="10" max="250" label="selected variant seq length out" help="sequence length to print from either side of selected variants (default: 50)" /> - - <param name="output" type="text" size="30" value="cheripic_results" label="tag for output filename" help="write a tag to include with output filename" /> </inputs> <outputs> - <data name="output_1" format="txt" file="${output}_selected_hme_variants.txt" /> - <data name="output_2" format="txt" file="${output}_selected_bfr_variants.txt" /> + <data name="output1" format="txt" from_work_dir="output_log.txt" label="cheripic log file" /> + <data name="output2" format="txt" from_work_dir="cheripic_results_selected_hme_variants.txt" label="selected hmes variants" /> + <data name="output3" format="txt" from_work_dir="cheripic_results_selected_bfr_variants.txt" label="selected bfr variants" > + <filter>polyploidy == "true"</filter> + </data> </outputs> <tests> <test> <param name="assembly" value="picked_fasta.fa" ftype="fasta" /> @@ -152,31 +171,40 @@ **cheripic parameter list** OPTIONS: -f, --assembly Assembly file in FASTA format - -F, --input-format bulk and parent alignment file format types - set either pileup or bam (default: pileup) + -F, --input-format bulk and parent alignment file format types - set either pileup or bam or vcf (default: pileup) -a, --mut-bulk Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1 + --mut-bulk-vcf vcf file for variants from mutant/trait of interest bulk 1 -b, --bg-bulk Pileup or sorted BAM file alignments from background/wildtype bulk 2 - --output Directory to store results, will be created if not existing (default: cheripic_results) + --bg-bulk-vcf vcf file for variants from background/wildtype bulk 2 + --output custom name tag to include in the output file name (default: cheripic_results) --loglevel Choose any one of "info / warn / debug" level for logs generated (default: debug) --hmes-adjust factor added to snp count of each contig to adjust for hme score calculations (default: 0.5) --htlow lower level for categorizing heterozygosity (default: 0.2) --hthigh high level for categorizing heterozygosity (default: 0.9) - --mindepth minimum read depth to conisder a position for variant calls (default: 6) + --mindepth minimum read depth at a position to consider for variant calls (default: 6) + --max-d-multiple multiplication factor for average coverage to calculate maximum read coverage + if set zero no calculation will be made from bam file. + setting this value will override user set max depth (Default: 5) + --maxdepth maximum read depth at a position to consider for variant calls + if set to zero no user max depth will be used (default: 0) --min-non-ref-count minimum read depth supporting non reference base at each position (default: 3) --min-indel-count-support minimum read depth supporting an indel at each position (default: 3) --ambiguous-ref-bases including variant at completely ambiguous bases in the reference -q, --mapping-quality minimum mapping quality of read covering the position (default: 20) -Q, --base-quality minimum base quality of bases covering the position (default: 15) --noise praportion of reads for a variant to conisder as noise (default: 0.1) --cross-type type of cross used to generated mapping population - back or out (default: back) --use-all-contigs option to select all contigs or only contigs containing variants for analysis - --include-low-hmes option to include or discard variants from contigs with low hme-score or bfr score to list in the final output + --include-low-hmes option to include or discard variants from contigs with + low hme-score or bfr score to list in the final output --polyploidy Set if the data input is from polyploids -p, --mut-parent Pileup or sorted BAM file alignments from mutant/trait of interest parent (default: ) -r, --bg-parent Pileup or sorted BAM file alignments from background/wildtype parent (default: ) + -R, --repeats-file repeat masker output file for the assembly (default: ) --bfr-adjust factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05) --sel-seq-len sequence length to print from either side of selected variants (default: 50) ------ @@ -188,9 +216,9 @@ </help> <citations> - <citation type="doi">10.1093/bioinformatics/btg1080</citation> + <citation type="doi">spaceholder</citation> </citations> </tool>