Repository 'bcftools'
hg clone https://testtoolshed.g2.bx.psu.edu/repos/wrtz/bcftools

Changeset 5:0e3e6581e6b1 (2016-01-14)
Previous changeset 4:2cffdec901f5 (2016-01-14) Next changeset 6:24fc012c3f0e (2016-01-14)
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bcftools_norm.xml
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diff -r 2cffdec901f5 -r 0e3e6581e6b1 bcftools_norm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_norm.xml Thu Jan 14 17:47:32 2016 -0500
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b'@@ -0,0 +1,153 @@\n+<tool id="bcftools_norm" name="BCFtools norm" version="1.0.0">\n+    <description>Left-align and normalize indels, check if REF alleles match reference, change multiallelic format</description>\n+    <command>\n+        #if str( $input_file_index ) != "None":\n+            ln -s -f $input input_file.${input.ext} &amp;&amp;\n+            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;\n+        #end if\n+        #if str( $fasta_ref_cond.set_fasta_ref ) == "True":\n+            #if str( $fasta_ref_cond.fasta_ref_index ) != "None":\n+                ln -s -f $fasta_ref_cond.fasta_ref fasta_ref_file.${fasta_ref.ext}.fa &amp;&amp;\n+                ln -s -f $fasta_ref_cond.fasta_ref_index fasta_ref_file.${fasta_ref.ext}.fa.fai &amp;&amp;\n+            #end if\n+        #end if\n+        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools norm                    \n+        --output "${output_file}"\n+        --output-type "${output_type}"\n+        #if str( $regions_file ) != "None":\n+            --regions-file "${regions_file}"\n+        #end if\n+        #if str( $regions ) != "":\n+            --regions "${regions}"\n+        #end if\n+        #if str( $targets_file ) != "None":\n+            --targets-file "${targets_file}"\n+        #end if\n+        #if str( $targets ) != "":\n+            --targets "${targets}"\n+        #end if\n+        #if str( $check_ref_cond.set_check_ref ) == "True":\n+            #if str( $check_ref_cond.warn ) == "true":\n+                #if str( $check_ref_cond.check_ref ) == "None":\n+                    --check-ref "w"\n+                #else\n+                    --check-ref "w${check_ref_cond.check_ref}"\n+                #end if\n+            #else\n+                --check-ref "${check_ref_cond.check_ref}"\n+            #end if\n+        #end if\n+        #if str( $fasta_ref_cond.set_fasta_ref ) == "True":\n+            #if str( $fasta_ref_cond.fasta_ref_index ) != "None":\n+                --fasta-ref "fasta_ref_file.${fasta_ref.ext}.fa"\n+            #else\n+                --fasta-ref "${fasta_ref}"\n+            #end if\n+        #end if\n+        #if str( $multiallelics_cond.set_multiallelics ) == "True":\n+            #if str( $multiallelics_cond.minus_or_plus ) == "minus":\n+                #if str ( $multiallelics_cond.multiallelics ) != "None":\n+                    --multiallelics "-${multiallelics_cond.multiallelics}"\n+                #else\n+                    --multiallelics "-"\n+                #end if\n+            #else\n+                #if str ( $multiallelics_cond.multiallelics ) != "None":\n+                    --multiallelics "+${multiallelics_cond.multiallelics}"\n+                #else\n+                    --multiallelics "+"\n+                #end if\n+            #end if\n+        #end if\n+        #if str( $rm_dup ) != "None":\n+            --rm-dup "${rm_dup}"\n+        #end if\n+        ${do_not_normalize}\n+        ${strict_filter}\n+        #if str( $site_win ) != "":\n+            --site-win "${site_win}"\n+        #end if\n+        #if str( $input_file_index ) != "None":\n+            input_file.${input.ext}\n+        #else\n+            $input\n+        #end if\n+    </command>\n+    <inputs>\n+        <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>\n+        <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>\n+        <param name="output_type" type="select" label="Output data type" help="-O">\n+            <option value="v" selected="true">VCF</option>\n+            <option value="b">BCF</option>\n+        </param>\n+        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with col'..b'ram name="do_not_normalize" type="boolean" checked="False" truevalue="--do-not-normalize" falsevalue="" label="Turn off indel normalization" help="-N. Indel normalization automatically occurs when FASTA reference is used. Use this option to disable this behavior." />\n+        <conditional name="check_ref_cond">\n+            <param name="set_check_ref" type="boolean" checked="False" label="Check REF" help="-c. Choose action when an incorrect or missing REF allele is encountered." />\n+            <when value="true">\n+                <param name="check_ref" type="select" optional="True" label="Action" help="Action when an incorrect or missing REF allele is encountered.">\n+                    <option value="e">Exit program</option>\n+                    <option value="x">Exclude incorrect/missing sites</option>\n+                    <option value="s">Set or fix incorrect/missing sites (requires FASTA reference)</option>\n+                </param>\n+                <param name="warn" type="boolean" checked="False" label="Warn" help="Warn when an incorrect or missing REF allele is encountered." />\n+            </when>\n+        </conditional>\n+        <param name="rm_dup" type="select" optional="True" label="Remove duplicates" help="-d. For given variant type, if a record is present in multiple files, output only the first instance.">\n+            <option value="snps">SNPs</option>\n+            <option value="indels">Indels</option>\n+            <option value="both">Both (SNPs and indels)</option>\n+            <option value="any">Any</option>\n+        </param>\n+        <conditional name="multiallelics_cond">\n+            <param name="set_multiallelics" type="boolean" checked="False" label="Modify multiallelic sites" help="-m. Split multiallelic sites into biallelic records, or join biallelic sites into multiallelic records." />\n+            <when value="true">\n+                <param name="minus_or_plus" type="select" label="Split or join">\n+                    <option value="minus" selected="true">Split multiallelic sites into biallelic records</option>    \n+                    <option value="plus">Join biallelic sites into multiallelic records</option>\n+                </param>      \n+                <param name="multiallelics" type="select" optional="True" label="Sites to split/join" help="">\n+                    <option value="snps">SNPs (only SNP records are split/joined)</option>\n+                    <option value="indels">Indels (only indel records are split/joined)</option>\n+                    <option value="both">Both (SNPs and indels are merged separately into two records)</option>\n+                    <option value="any">Any (SNPs and indels are merged into a single record)</option>\n+                </param>\n+            </when>\n+        </conditional>\n+        <param name="strict_filter" type="boolean" checked="False" truevalue="--strict-filter" falsevalue="" label="Strict PASS filter" help="-s. When merging biallelics into multiallelics, merged site has value PASS only if all sites being merged have value PASS." />\n+        <param name="site_win" type="integer" optional="true" label="Position window" help="-w. Maximum distance between two records to consider when locally sorting variants which changed position during the realignment." />\n+    </inputs>\n+    <outputs>\n+        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">\n+            <change_format>\n+                <when input="output_type" value="b" format="bcf" />\n+            </change_format>\n+        </data>\n+    </outputs>\n+    <help>\n+**About this tool**\n+\n+**BCFtools norm**: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows, recover multiallelics from multiple rows. Left-alignment and normalization will only be applied if the --fasta-ref option is supplied.\n+\n+Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.\n+  </help>\n+</tool>\n+\n'