Mercurial > repos > dave > lofreq_call
diff lofreq_call.xml @ 0:b37a6b94e9fe draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
| author | dave |
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| date | Wed, 27 Nov 2019 15:25:33 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lofreq_call.xml Wed Nov 27 15:25:33 2019 +0000 @@ -0,0 +1,200 @@ +<tool id="lofreq_call" name="Call variants" version="@WRAPPER_VERSION@0"> + <description>with LoFreq</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ## prepare reference genome and mapped reads input + @PREPARE_REF@ + ln -s '$reads' reads.bam && + ln -s -f '${reads.metadata.bam_index}' reads.bam.bai && + + ## call variants with lofreq + + ## make lofreq stick to tool contract by + ## generating tmp output inside job working dir + mkdir pp-tmp && + export TMPDIR=pp-tmp && + + lofreq call-parallel + + --ref '$reference_fasta_fn' --out variants.vcf --pp-threads \${GALAXY_SLOTS:-1} + + #if $advanced_options.option_selector == 'yes' + #if $advanced_options.regions.bed + --bed '$advanced_options.regions.bed' + #end if + #if $advanced_options.source_qual.ign_vcf + --ign-vcf '$advanced_options.source_qual.ign_vcf' + #end if + #if $advanced_options.regions.region + --region $advanced_options.regions.region + #end if + #if $advanced_options.pval.bonf + --bonf $advanced_options.pval.bonf + #else + --bonf dynamic + #end if + --min-bq $advanced_options.bc_quals.min_bq + --min-alt-bq $advanced_options.bc_quals.min_alt_bq + --def-alt-bq $advanced_options.bc_quals.def_alt_bq + --min-jq $advanced_options.bc_quals.min_jq + --min-alt-jq $advanced_options.bc_quals.min_alt_jq + --def-alt-jq $advanced_options.bc_quals.def_alt_jq + --min-mq $advanced_options.map_quals.min_mq + --max-mq $advanced_options.map_quals.max_mq + --def-nm-q $advanced_options.source_qual.def_nm_q + --sig $advanced_options.pval.sig + --min-cov $advanced_options.misc.min_cov + --max-depth $advanced_options.misc.max_depth + $advanced_options.align_quals.no_baq + $advanced_options.align_quals.no_idaq + $advanced_options.align_quals.del_baq + $advanced_options.align_quals.no_ext_baq + $advanced_options.map_quals.no_mq + $advanced_options.indels.call_indels + $advanced_options.indels.only_indels + $advanced_options.source_qual.src_qual + $advanced_options.misc.use_orphan + $advanced_options.misc.plp_summary_only + $advanced_options.misc.no_default_filter + #end if + + reads.bam 2>&1 + + ## in case of errors add the log files produced + ## by the parallel workers to stderr + || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code) + ]]></command> + <inputs> + <param type="data" name="reads" format="bam" label="Input reads in BAM format" /> + <expand macro="reference_interface" /> + <conditional name="advanced_options"> + <param name="option_selector" type="select" label="Advanced options"> + <option value="no" selected="true">Use defaults</option> + <option value="yes">Specify parameters</option> + </param> + <when value="no" /> + <when value="yes"> + <section name="regions" title="Regions" expanded="false"> + <param argument="--bed" type="data" format="bed" optional="true" label="BED file with regions to examine" /> + <param argument="--region" type="text" label="Limit calls to this region" /> + </section> + <section name="bc_quals" title="Base-calling quality" expanded="false"> + <param name="min_bq" argument="--min-bq" type="integer" value="6" label="Mimimum baseQ" /> + <param name="min_alt_bq" argument="--min-alt-bq" type="integer" value="6" label="Mimimum baseQ for alternate bases" /> + <param name="def_alt_bq" argument="--def-alt-bq" type="integer" value="0" label="Overwrite baseQs of alternate bases with this value" /> + <param name="min_jq" argument="--min-jq" type="integer" value="0" label="Minimum joinedQ" /> + <param name="min_alt_jq" argument="--min-alt-jq" type="integer" value="0" label="Minimum joinedQ for alternate bases" /> + <param name="def_alt_jq" argument="--def-alt-jq" type="integer" value="0" label="Overwrite joinedQs of alternate bases with this value" /> + </section> + <section name="align_quals" title="Base alignment quality" expanded="false"> + <param name="no_baq" argument="--no-baq" type="boolean" truevalue="--no-baq" falsevalue="" label="Disable use of base-alignment quality" /> + <param name="no_idaq" argument="--no-idaq" type="boolean" truevalue="--no-idaq" falsevalue="" label="Don't use IDAQ values" /> + <param name="del_baq" argument="--del-baq" type="boolean" truevalue="--del-baq" falsevalue="" label="Delete pre-existing BAQ values" help="Computes BAQ values regardless of their presence in the input BAM" /> + <param name="no_ext_baq" argument="--no-ext-baq" type="boolean" truevalue="--no-ext-baq" falsevalue="" label="Do not use external BAQ" help="Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)" /> + </section> + <section name="map_quals" title="Mapping quality" expanded="false"> + <param name="min_mq" argument="--min-mq" type="integer" value="0" label="Minimum mapping quality" /> + <param name="max_mq" argument="--max-mq" type="integer" value="255" label="Maximum mapping quality" /> + <param name="no_mq" argument="--no-mq" type="boolean" truevalue="--src-qua" falsevalue="" label="Don't merge mapping quality" /> + </section> + <section name="indels" title="Indels" expanded="false"> + <param name="call_indels" argument="--call-indels" type="boolean" truevalue="--call-indels" falsevalue="" label="Enable indel calls" help="Note: This adds a preprocessing step to include indel alignment qualities" /> + <param name="only_indels" argument="--only-indels" type="boolean" truevalue="--only-indels" falsevalue="" label="Only call indels; no SNVs" /> + </section> + <section name="source_qual" title="Source quality" expanded="false"> + <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf" optional="true" label="Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas" /> + <param name="src_qual" argument="--src-qual" type="boolean" truevalue="--src-qua" falsevalue="" label="Enable computation of source quality" /> + <param name="def_nm_q" argument="--def-nm-q" type="integer" value="-1" label="Replace non-match base qualities with this value" /> + </section> + <section name="pval" title="P-values" expanded="false"> + <param argument="--sig" type="float" value="0.01" label="P-Value cutoff" /> + <param argument="--bonf" type="integer" optional="true" label="Bonferroni factor" help="Leave unset to increase the factor per performed test or specify a factor here" /> + </section> + <section name="misc" title="Other options" expanded="false"> + <param name="min_cov" argument="--min-cov" type="integer" value="1" label="Test only positions having at least this coverage" /> + <param name="max_depth" argument="--max-depth" type="integer" value="1000000" label="Cap coverage at this depth" /> + <param name="use_orphan" argument="--use-orphan" type="boolean" truevalue="--use-orphan" falsevalue="" label="Count anomalous read pairs" /> + <param name="plp_summary_only" argument="--plp-summary-only" type="boolean" truevalue="--plp-summary-only" falsevalue="" label="No variant calling, just output pileup summary per column" /> + <param name="no_default_filter" argument="--no-default-filter" type="boolean" truevalue="--no-default-filter" falsevalue="" label="Don't run default 'lofreq filter' automatically after calling variants" /> + </section> + </when> + </conditional> + </inputs> + <outputs> + <data name="variants" from_work_dir="variants.vcf" format="vcf" /> + </outputs> + <tests> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="ref_selector" value="history" /> + <param name="ref" ftype="fasta" value="pBR322.fa" /> + <output name="variants" file="call-out1.vcf" lines_diff="4" /> + </test> + </tests> + <help><![CDATA[ +lofreq call: call variants from BAM file + +Usage: lofreq call [options] in.bam + +Options: + +- Reference: + -f | --ref FILE Indexed reference fasta file (gzip supported) [null] + +- Output: + -o | --out FILE Vcf output file [- = stdout] + +- Regions: + -r | --region STR Limit calls to this region (chrom:start-end) [null] + -l | --bed FILE List of positions (chr pos) or regions (BED) [null] + +- Base-call quality: + -q | --min-bq INT Skip any base with baseQ smaller than INT [6] + -Q | --min-alt-bq INT Skip alternate bases with baseQ smaller than INT [6] + -R | --def-alt-bq INT Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0] + -j | --min-jq INT Skip any base with joinedQ smaller than INT [0] + -J | --min-alt-jq INT Skip alternate bases with joinedQ smaller than INT [0] + -K | --def-alt-jq INT Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0] + +- Base-alignment (BAQ) and indel-aligment (IDAQ) qualities: + -B | --no-baq Disable use of base-alignment quality (BAQ) + -A | --no-idaq Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging) + -D | --del-baq Delete pre-existing BAQ values, i.e. compute even if already present in BAM + -e | --no-ext-baq Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag) + +- Mapping quality: + -m | --min-mq INT Skip reads with mapping quality smaller than INT [0] + -M | --max-mq INT Cap mapping quality at INT [255] + -N | --no-mq Don't merge mapping quality in LoFreq's model + +- Indels: + --call-indels Enable indel calls (note: preprocess your file to include indel alignment qualities!) + --only-indels Only call indels; no SNVs + +- Source quality: + -s | --src-qual Enable computation of source quality + -S | --ign-vcf FILE Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas + -T | --def-nm-q INT If >= 0, then replace non-match base qualities with this default value [-1] + +- P-values: + -a | --sig P-Value cutoff / significance level [0.010000] + -b | --bonf Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic'] + +- Misc.: + -C | --min-cov INT Test only positions having at least this coverage [1] + (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done) + -d | --max-depth INT Cap coverage at this depth [1000000] + --illumina-1.3 Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded + --use-orphan Count anomalous read pairs (i.e. where mate is not aligned properly) + --plp-summary-only No variant calling. Just output pileup summary per column + --no-default-filter Don't run default 'lofreq filter' automatically after calling variants + --force-overwrite Overwrite any existing output + --verbose Be verbose + --debug Enable debugging + +]]></help> + <expand macro="citations" /> +</tool>