# HG changeset patch
# User wrtz
# Date 1452811710 18000
# Node ID 48695211cd658bebc14135b0606325e0cf994488
# Parent  792289298f4bba588f946556f63f735966013c22
Deleted selected files

diff -r 792289298f4b -r 48695211cd65 bcftools_annotate.xml
--- a/bcftools_annotate.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +0,0 @@
-<tool id="bcftools_annotate" name="BCFtools annotate" version="1.0.0">
-    <description>Add or remove annotations</description>
-    <command>
-        #if str( $input_file_index ) != "None":
-            ln -s -f $input input_file.${input.ext} &amp;&amp;
-            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
-        #end if
-        #if str( $annotations_cond.set_annotations ) == "True":
-            ln -s -f $annotations_cond.annotations annot_file.${annotations_cond.annotations.ext} &amp;&amp;
-            ln -s -f $annotations_cond.annotations_index annot_file.${annotations_cond.annotations.ext}.tbi &amp;&amp;
-        #end if
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools annotate
-        --output "${output_file}"
-        --output-type "${output_type}"
-        #if str( $regions_file ) != "None":
-            --regions-file "${regions_file}"
-        #end if
-        #if str( $annotations_cond.set_annotations ) == "True":
-            --annotations annot_file.${annotations_cond.annotations.ext}
-            #if str( $annotations_cond.columns ) != "":
-                --columns "${annotations_cond.columns}"
-            #end if
-            #if str( $annotations_cond.mark_sites_cond.set_mark_sites ) == "True":
-                --mark-sites
-                #if str( $annotations_cond.mark_sites_cond.present_or_absent ) == "present":
-                    "+${annotations_cond.mark_sites_cond.new_tag}"
-                #else
-                    "-${annotations_cond.mark_sites_cond.new_tag}"
-                #end if
-            #end if
-        #end if
-        #if str( $regions ) != "":
-            --regions "${regions}"
-        #end if
-       #if str( $samples_file ) != "None":
-            --samples-file "${samples_file}"
-        #end if
-        #if str( $samples ) != "":
-            --samples "${samples}"
-        #end if
-        #if str( $header_lines ) != "None":
-            --header-lines "${header_lines}"
-        #end if
-        #if str( $expr_cond.set_expr ) == "True":
-            #if str( $expr_cond.include_or_exclude ) == "include":
-                --include "${expr_cond.expr}"
-            #else
-                --exclude "${expr_cond.expr}"
-            #end if
-        #end if
-        #if str( $rename_chrs ) != "None":
-            --rename-chrs "${rename_chrs}"
-        #end if
-        #if str( $remove ) != "":
-            --remove "${remove}"
-        #end if
-
-        #if str( $input_file_index ) != "None":
-            input_file.${input.ext}
-        #else
-            $input
-        #end if
-    </command>
-    <inputs>
-        <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."/>
-        <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."/>
-        <param name="output_type" type="select" label="Output data type" help="-O">
-            <option value="v" selected="true">VCF</option>
-            <option value="b">BCF</option>
-        </param>
-        <conditional name="annotations_cond">
-            <param name="set_annotations" type="boolean" checked="False" label="Set annotation file" help="-a, -c, -m"/>
-            <when value="true">
-                <param name="annotations" type="data" label="Compressed annotation file" help="-a. Bgzip-compressed VCF/ BED/ tab-delimited file with annotations. Run Bgzip Galaxy tool to compress annotation file."/>
-                <param name="annotations_index" type="data" label="Compressed annotation file index" help="Tabix-generated index for annotation file. Run Tabix Galaxy tool on bgzipped annotation file to create index."/>
-                <param name="columns" type="text" label="Annotation file columns" help="-c. Comma-separated list of columns or tags to carry over from the annotation file." />
-
-                <conditional name="mark_sites_cond">
-                    <param name="set_mark_sites" type="boolean" checked="False" label="Mark present/absent sites" help="-m. Annotate sites which are present or absent in the annotation file with a new INFO/TAG flag. Note: BCFtools has not implemented this yet for VCF files."/>
-                    <when value="true">
-                        <param name="present_or_absent" type="select" label="Mark present or absent sites">
-                            <option value="present">Present</option>
-                            <option value="absent">Absent</option>
-                        </param>
-                        <param name="new_tag" type="text" label="New INFO/TAG flag" />
-                    </when>
-                </conditional>
-
-            </when>
-        </conditional>
-
-        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="regions" type="text" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
-        <param name="samples" type="text" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
-        <param name="header_lines" type="data" optional="true" label="Header lines" help="-h. File containing lines to append to VCF header."/>
-        <conditional name="expr_cond">
-            <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, -e. Include/ exclude sites for which expression is true. Must use valid expression."/>
-            <when value="true">
-                <param name="include_or_exclude" type="select" label="Include or exclude by expression">
-                    <option value="include">Include</option>
-                    <option value="exclude">Exclude</option>
-                </param>
-                <param name="expr" type="text" label="Expression">
-                    <sanitizer invalid_char="">
-                        <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
-                    </sanitizer>
-                </param>
-            </when>
-        </conditional>
-        <param name="rename_chrs" type="data" optional="true" label="Rename chromosomes" help="--rename-chrs. File containing chromosome renaming map, with &quot;old_name new_name\n&quot; pairs separated by whitespaces, each on a separate line."/>
-        <param name="remove" type="text" label="List of annotations to remove" help="-x. Comma-separated list of annotations to remove." />
-    </inputs>
-    <outputs>
-        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="output_type" value="b" format="bcf" />
-            </change_format>
-        </data>
-    </outputs>
-    <help>
-**About this tool**
-
-**BCFtools annotate**: Add or remove annotations.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
\ No newline at end of file
diff -r 792289298f4b -r 48695211cd65 bcftools_filter.xml
--- a/bcftools_filter.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-<tool id="bcftools_filter" name="BCFtools filter" version="1.0.0">
-    <description>Apply fixed-threshold filters</description>
-    <command>
-        #if str( $input_file_index ) != "None":
-            ln -s -f $input input_file.${input.ext} &amp;&amp;
-            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
-        #end if
-
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools filter                    
-        --output "${output_file}"
-        --output-type "${output_type}"
-        #if str( $regions_file ) != "None":
-            --regions-file "${regions_file}"
-        #end if
-        #if str( $regions ) != "":
-            --regions "${regions}"
-        #end if
-        #if str( $targets_file ) != "None":
-            --targets-file "${targets_file}"
-        #end if
-        #if str( $targets ) != "":
-            --targets "${targets}"
-        #end if
-        #if str( $expr_cond.set_expr ) == "True":
-            #if str( $expr_cond.include_or_exclude ) == "include":
-                --include "${expr_cond.expr}"
-            #else
-                --exclude "${expr_cond.expr}"
-            #end if
-        #end if
-        #if str( $mode_plus ) == "true":
-            #if str( $mode_x ) == "true":
-                --mode +x
-            #else
-                --mode +
-            #end if
-        #elif str( $mode_x ) == "true"
-            --mode x
-        #end if
-        #if str( $soft_filter_cond.set_soft_filter ) == "True":
-            #if str( $soft_filter_cond.string_or_plus_cond.string_or_plus ) == "use_plus":
-                --soft-filter +
-            #else
-                --soft-filter "${soft_filter_cond.string_or_plus_cond.str}"
-            #end if
-        #end if
-        #if str( $set_gts_cond.set_gts ) == "True":
-            #if str( $set_gts_cond.gts ) == "period":
-                --set-GTs .
-            #else
-                --set-GTs 0
-            #end if
-        #end if
-
-        #if str( $input_file_index ) != "None":
-            input_file.${input.ext}
-        #else
-            $input
-        #end if
-    </command>
-    <inputs>
-        <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."/>
-        <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."/>
-        <param name="output_type" type="select" label="Output data type">
-            <option value="v" selected="true">VCF</option>
-            <option value="b">BCF</option>
-        </param>
-        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="regions" type="text" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="targets" type="text" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
-            </sanitizer>
-        </param>
-        <conditional name="expr_cond">
-            <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, e. Include/ exclude sites for which expression is true. Must use valid expression."/>
-            <when value="true">
-                <param name="include_or_exclude" type="select" label="Include or exclude by expression">
-                    <option value="include">Include</option>
-                    <option value="exclude">Exclude</option>
-                </param>
-                <param name="expr" type="text" label="Expression">
-                    <sanitizer invalid_char="">
-                        <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
-                    </sanitizer>
-                </param>
-            </when>
-        </conditional>
-        <param name="mode_x" type="boolean" checked="False" label="For sites that pass filter, reset filter to &quot;PASS&quot;" help="-m x. Default: When FILTER string is empty, set filter to &quot;PASS&quot;. Do not change FILTER string otherwise."/>
-        <param name="mode_plus" type="boolean" checked="False" label="For sites that fail filter, append new FILTER string to existing FILTER string" help="-m +. Default: Replace existing FILTER string with new FILTER string."/>
-        <conditional name="soft_filter_cond">
-            <param name="set_soft_filter" type="boolean" checked="False" label="Annotate FILTER column" help="-s"/>
-            <when value="true">
-                <conditional name="string_or_plus_cond">
-                    <param name="string_or_plus" type="select" label="Annotation string">
-                        <option value="use_plus" selected="true">Annotate with a pre-generated unique string  (&quot;Filter1&quot;, &quot;Filter2&quot;, etc.)</option>
-                        <option value="use_str">Choose annotation string</option>
-                    </param>
-                    <when value="use_str">
-                        <param name="str" type="text" label="String to annotate with" />
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-        <conditional name="set_gts_cond">
-            <param name="set_gts" type="boolean" checked="False" label="Set genotype of samples that fail filter" help="-S"/>
-            <when value="true">
-                <param name="gts" type="select" label="Genotype of failed samples">
-                    <option value="period" selected="true">.</option>
-                    <option value="ref_allele">Reference allele</option>
-                </param>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="output_type" value="b" format="bcf" />
-            </change_format>
-        </data>
-    </outputs>
-    <help>
-**About this tool**
-
-**BCFtools filter**: Apply fixed-threshold filters.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
\ No newline at end of file
diff -r 792289298f4b -r 48695211cd65 bcftools_merge.xml
--- a/bcftools_merge.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-<tool id="bcftools_merge" name="BCFtools merge" version="1.0.0">
-    <description>Merge multiple VCF/BCF files</description>
-    <command>
-        #for $i, $inp in enumerate( $inputs ):
-            #if str( $inp.input_file_index ) != "None":
-                ln -s -f "${inp.input}" "input_file_${i}.${inp.input.ext}" &amp;&amp;
-                ln -s -f "${inp.input_file_index}" "input_file_${i}.${inp.input.ext}.tbi" &amp;&amp;
-            #end if
-        #end for
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools merge                   
-        --output "${output_file}"
-        --output-type "${output_type}"
-        #if str( $regions_file ) != "None":
-            --regions-file "${regions_file}"
-        #end if
-        #if str( $regions ) != "":
-            --regions "${regions}"
-        #end if
-        ${force_samples}
-        #if str( $info_rules ) != "":
-            --info-rules "${info_rules}"
-        #end if
-        #if str( $merge ) != "None":
-            --merge "${merge}"
-        #end if
-
-        #for $i, $inp in enumerate( $inputs ):
-            #if str( $inp.input_file_index ) != "None":
-                "input_file_${i}.${inp.input.ext}"
-            #else
-                "${inp.input}"
-            #end if
-        #end for
-    </command>
-    <inputs>
-        <repeat name="inputs" title="Input files to merge" default="2" min="2">
-            <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."/>
-            <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."/>
-        </repeat>
-        <param name="output_type" type="select" label="Output data type" help="-O">
-            <option value="v" selected="true">VCF</option>
-            <option value="b">BCF</option>
-        </param>
-        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="regions" type="text" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="info_rules" type="text" optional="True" label="Rules for merging INFO fields" help="-i. Format: &quot;-|TAG:METHOD[,...]&quot;. METHOD can be either &quot;sum&quot;, &quot;avg&quot;, &quot;min&quot;, &quot;max&quot;, or &quot;join&quot;. Default rule string is &quot;DP:sum,DP4:sum&quot;. &quot;-&quot; disables the default rules." />
-        <param name="force_samples" type="boolean" checked="False" truevalue="--force-samples" falsevalue="" label="Force samples" help="--force-samples. Proceed even if the merged files contain duplicate sample names. Duplicate sample names are resolved by prepending file index to the conflicting sample name." />
-        <param name="merge" type="select" optional="True" label="Multiallelic record types" help="-m. Control what types of multiallelic records can be created.">
-            <option value="none">None (Output multiple records instead of multiallelic records)</option>
-            <option value="snps">SNPs (Allow multiallelic SNP records)</option>
-            <option value="indels">Indels (Allow multiallelic indel records)</option>
-            <option value="both">Both (Allow both SNP and indel multiallelic records)</option>
-            <option value="all">All (Allow SNP records to be merged with indel records)</option>
-            <option value="id">ID (Merge by ID)</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="output_type" value="b" format="bcf" />
-            </change_format>
-        </data>
-    </outputs>
-    <help>
-**About this tool**
-
-**BCFtools merge**: Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file. For example, when merging file A.vcf.gz containing samples S1, S2 and S3 and file B.vcf.gz containing samples S3 and S4, the output file will contain four samples named S1, S2, S3, 2:S3 and S4.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
\ No newline at end of file
diff -r 792289298f4b -r 48695211cd65 bcftools_norm.xml
--- a/bcftools_norm.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-<tool id="bcftools_norm" name="BCFtools norm" version="1.0.0">
-    <description>Left-align and normalize indels, check if REF alleles match reference, change multiallelic format</description>
-    <command>
-        #if str( $input_file_index ) != "None":
-            ln -s -f $input input_file.${input.ext} &amp;&amp;
-            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
-        #end if
-        #if str( $fasta_ref_cond.set_fasta_ref ) == "True":
-            #if str( $fasta_ref_cond.fasta_ref_index ) != "None":
-                ln -s -f $fasta_ref_cond.fasta_ref fasta_ref_file.${fasta_ref.ext}.fa &amp;&amp;
-                ln -s -f $fasta_ref_cond.fasta_ref_index fasta_ref_file.${fasta_ref.ext}.fa.fai &amp;&amp;
-            #end if
-        #end if
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools norm                    
-        --output "${output_file}"
-        --output-type "${output_type}"
-        #if str( $regions_file ) != "None":
-            --regions-file "${regions_file}"
-        #end if
-        #if str( $regions ) != "":
-            --regions "${regions}"
-        #end if
-        #if str( $targets_file ) != "None":
-            --targets-file "${targets_file}"
-        #end if
-        #if str( $targets ) != "":
-            --targets "${targets}"
-        #end if
-        #if str( $check_ref_cond.set_check_ref ) == "True":
-            #if str( $check_ref_cond.warn ) == "true":
-                #if str( $check_ref_cond.check_ref ) == "None":
-                    --check-ref "w"
-                #else
-                    --check-ref "w${check_ref_cond.check_ref}"
-                #end if
-            #else
-                --check-ref "${check_ref_cond.check_ref}"
-            #end if
-        #end if
-        #if str( $fasta_ref_cond.set_fasta_ref ) == "True":
-            #if str( $fasta_ref_cond.fasta_ref_index ) != "None":
-                --fasta-ref "fasta_ref_file.${fasta_ref.ext}.fa"
-            #else
-                --fasta-ref "${fasta_ref}"
-            #end if
-        #end if
-        #if str( $multiallelics_cond.set_multiallelics ) == "True":
-            #if str( $multiallelics_cond.minus_or_plus ) == "minus":
-                #if str ( $multiallelics_cond.multiallelics ) != "None":
-                    --multiallelics "-${multiallelics_cond.multiallelics}"
-                #else
-                    --multiallelics "-"
-                #end if
-            #else
-                #if str ( $multiallelics_cond.multiallelics ) != "None":
-                    --multiallelics "+${multiallelics_cond.multiallelics}"
-                #else
-                    --multiallelics "+"
-                #end if
-            #end if
-        #end if
-        #if str( $rm_dup ) != "None":
-            --rm-dup "${rm_dup}"
-        #end if
-        ${do_not_normalize}
-        ${strict_filter}
-        #if str( $site_win ) != "":
-            --site-win "${site_win}"
-        #end if
-        #if str( $input_file_index ) != "None":
-            input_file.${input.ext}
-        #else
-            $input
-        #end if
-    </command>
-    <inputs>
-        <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."/>
-        <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."/>
-        <param name="output_type" type="select" label="Output data type" help="-O">
-            <option value="v" selected="true">VCF</option>
-            <option value="b">BCF</option>
-        </param>
-        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="regions" type="text" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="targets" type="text" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
-            </sanitizer>
-        </param>
-        <conditional name="fasta_ref_cond">
-            <param name="set_fasta_ref" type="boolean" checked="False" label="Specify FASTA reference sequence" help="-f" />
-            <when value="true">
-                <param name="fasta_ref" type="data" label="FASTA reference file" help="Reference sequence. Using this option turns on left-alignment and normalization. Set corresponding index below." />
-                <param name="fasta_ref_index" type="data" optional="True" label="FASTA reference index" help="Run Faidx (SAMtools) Galaxy tool on above reference file to create index. Errors can arise if this index is not specified." />
-            </when>
-        </conditional>
-        <param 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." />
-        <conditional name="check_ref_cond">
-            <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." />
-            <when value="true">
-                <param name="check_ref" type="select" optional="True" label="Action" help="Action when an incorrect or missing REF allele is encountered.">
-                    <option value="e">Exit program</option>
-                    <option value="x">Exclude incorrect/missing sites</option>
-                    <option value="s">Set or fix incorrect/missing sites (requires FASTA reference)</option>
-                </param>
-                <param name="warn" type="boolean" checked="False" label="Warn" help="Warn when an incorrect or missing REF allele is encountered." />
-            </when>
-        </conditional>
-        <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.">
-            <option value="snps">SNPs</option>
-            <option value="indels">Indels</option>
-            <option value="both">Both (SNPs and indels)</option>
-            <option value="any">Any</option>
-        </param>
-        <conditional name="multiallelics_cond">
-            <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." />
-            <when value="true">
-                <param name="minus_or_plus" type="select" label="Split or join">
-                    <option value="minus" selected="true">Split multiallelic sites into biallelic records</option>    
-                    <option value="plus">Join biallelic sites into multiallelic records</option>
-                </param>      
-                <param name="multiallelics" type="select" optional="True" label="Sites to split/join" help="">
-                    <option value="snps">SNPs (only SNP records are split/joined)</option>
-                    <option value="indels">Indels (only indel records are split/joined)</option>
-                    <option value="both">Both (SNPs and indels are merged separately into two records)</option>
-                    <option value="any">Any (SNPs and indels are merged into a single record)</option>
-                </param>
-            </when>
-        </conditional>
-        <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." />
-        <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." />
-    </inputs>
-    <outputs>
-        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="output_type" value="b" format="bcf" />
-            </change_format>
-        </data>
-    </outputs>
-    <help>
-**About this tool**
-
-**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.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
-
diff -r 792289298f4b -r 48695211cd65 bcftools_query.xml
--- a/bcftools_query.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-<tool id="bcftools_query" name="BCFtools query" version="1.0.0">
-    <description>Output VCF/BCF fields in user-defined format</description>
-    <command>
-        #if str( $input_file_index ) != "None":
-            ln -s -f $input input_file.${input.ext} &amp;&amp;
-            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
-        #end if
-
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools query                    
-        --output "${output_file}"
-        --format "${format}"
-        #if str( $regions_file ) != "None":
-            --regions-file "${regions_file}"
-        #end if
-        #if str( $regions ) != "":
-            --regions "${regions}"
-        #end if
-        #if str( $targets_file ) != "None":
-            --targets-file "${targets_file}"
-        #end if
-        #if str( $targets ) != "":
-            --targets "${targets}"
-        #end if
-        #if str( $samples_file ) != "None":
-            --samples-file "${samples_file}"
-        #end if
-        #if str( $samples ) != "":
-            --samples "${samples}"
-        #end if
-        #if str( $expr_cond.set_expr ) == "True":
-            #if str( $expr_cond.include_or_exclude ) == "include":
-                --include "${expr_cond.expr}"
-            #else
-                --exclude "${expr_cond.expr}"
-            #end if
-        #end if
-        #if str( $collapse ) != "None":
-            --collapse "${collapse}"
-        #end if
-        ${print_header}
-        ${list_samples}
-        ${allow_undef_tags}
-
-        #if str( $input_file_index ) != "None":
-            input_file.${input.ext}
-        #else
-            $input
-        #end if
-    </command>
-    <inputs>
-        <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
-        <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
-        <param name="format" type="text" label="Output format string (required)" help="-f. Example: &quot;%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n&quot;. See BCFtools documentation for more info.">
-            <sanitizer invalid_char="">
-                <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
-            </sanitizer>
-        </param>
-        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="regions" type="text" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="targets" type="text" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
-        <param name="samples" type="text" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
-        <conditional name="expr_cond">
-            <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, e. Include/ exclude sites for which expression is true. Must use valid expression."/>
-            <when value="true">
-                <param name="include_or_exclude" type="select" label="Include or exclude by expression">
-                    <option value="include">Include</option>
-                    <option value="exclude">Exclude</option>
-                </param>
-                <param name="expr" type="text" label="Expression">
-                    <sanitizer invalid_char="">
-                        <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
-                    </sanitizer>
-                </param>
-            </when>
-        </conditional>
-        <param name="collapse" optional="True" type="select" label="Collapse records" help="-c. Controls how to treat records with duplicate positions, and defines compatible records across multiple input files.">
-            <option value="some">Some (only records where some subset of ALT alleles match are compatible)</option>
-            <option value="all">All (all records are compatible, regardless of whether ALT alleles match)</option>
-            <option value="snps">SNPs (all SNP records are compatible, regardless of whether ALT alleles match) </option>
-            <option value="indels">Indels (all indel records are compatible, regardless of whether REF and ALT alleles match) </option>
-            <option value="both">Both (SNPs are compatible and indels are compatible)</option>
-        </param>
-        <param name="print_header" type="boolean" checked="False" truevalue="--print-header" falsevalue="" label="Print header" help="-H" />
-        <param name="list_samples" type="boolean" checked="False" truevalue="--list-samples" falsevalue="" label="Print sample names to stdout, then exit" help="-l" />
-        <param name="allow_undef_tags" type="boolean" checked="False" truevalue="--allow-undef-tags" falsevalue="" label="Allow undefined tags" help="-u. If there are undefined tags in the format string, print &quot;.&quot; instead of throwing an error." />
-    </inputs>
-    <outputs>
-        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}" />
-    </outputs>
-    <help>
-**About this tool**
-
-**BCFtools query**: Extract fields from VCF or BCF files and output them in user-defined format.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
\ No newline at end of file
diff -r 792289298f4b -r 48695211cd65 bcftools_reheader.xml
--- a/bcftools_reheader.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<tool id="bcftools_reheader" name="BCFtools reheader" version="1.0.0">
-    <description>Modify header of VCF/BCF files, change sample names</description>
-    <command>
-        #if str( $input_file_index ) != "None":
-            ln -s -f $input input_file.${input.ext} &amp;&amp;
-            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
-        #end if
-
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools reheader
-        --output "${output_file}"
-        #if str( $header ) != "None":
-            --header "${header}"
-        #end if
-        #if str( $samples ) != "None":
-            --samples "${samples}"
-        #end if
-        #if str( $input_file_index ) != "None":
-            input_file.${input.ext}
-        #else
-            $input
-        #end if
-    </command>
-    <inputs>
-        <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
-        <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
-        <param name="header" type="data" optional="True" label="New VCF header" help="-h"/>
-        <param name="samples" type="data" optional="True" label="New sample names" help="-s. Either new sample names, each on a separate line, in the same order as samples appear in the VCF file, or &quot;old_name new_name\n&quot; pairs separated by whitespaces, each on a separate line." />
-    </inputs>
-    <outputs>
-        <data name="output_file" format_source="input" label="${tool.name} on ${on_string}" />
-    </outputs>
-    <help>
-**About this tool**
-
-**BCFtools reheader**: Modify header of VCF/BCF files, change sample names.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
diff -r 792289298f4b -r 48695211cd65 bcftools_view.xml
--- a/bcftools_view.xml	Thu Jan 14 17:48:01 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,224 +0,0 @@
-<tool id="bcftools_view" name="BCFtools view" version="1.0.0">
-    <description>Convert, view, subset, and filter VCF/BCF files</description>
-    <command>
-        #if str( $input_file_index ) != "None":
-            ln -s -f $input input_file.${input.ext} &amp;&amp;
-            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
-        #end if
-        /Volumes/drive2/galaxy/dist/tools/bcftools/bcftools view
-        ${drop_genotypes}
-        ${header_only}
-        ${no_header}
-        --output-file "${output_file}"
-        --output-type "${output_type}"
-        #if str( $regions ) != "":
-            --regions "${regions}"
-        #end if
-        #if str( $targets ) != "":
-            --targets "${targets}"
-        #end if
-        #if str( $samples ) != "":
-            --samples "${samples}"
-        #end if
-        #if str( $regions_file ) != "None":
-            --regions-file "${regions_file}"
-        #end if
-        #if str( $targets_file ) != "None":
-            --targets-file "${targets_file}"
-        #end if
-        #if str( $samples_file ) != "None":
-            --samples-file "${samples_file}"
-        #end if
-        #if str( $apply_filters ) != "":
-            --apply-filters "${apply_filters}"
-        #end if
-        #if str( $min_ac_cond.set_min_ac ) == "True":
-            --min-ac $min_ac_cond.min_ac:$min_ac_cond.min_ac_type
-        #end if
-        #if str( $max_ac_cond.set_max_ac ) == "True":
-            --max-ac $max_ac_cond.max_ac:$max_ac_cond.max_ac_type
-        #end if
-        #if str( $min_af_cond.set_min_af ) == "True":
-            --min-af $min_af_cond.min_af:$min_af_cond.min_af_type
-        #end if
-        #if str( $max_af_cond.set_max_af ) == "True":
-            --max-af $max_af_cond.max_af:$max_af_cond.max_af_type
-        #end if
-        #if str( $expr_cond.set_expr ) == "True":
-            #if str( $expr_cond.include_or_exclude ) == "include":
-                --include "${expr_cond.expr}"
-            #else
-                --exclude "${expr_cond.expr}"
-            #end if
-        #end if
-        #if str( $genotype_cond.set_genotype ) == "True":
-            #if str( $genotype_cond.include_or_exclude ) == "include":
-                --genotype $genotype_cond.genotype
-            #else
-                --genotype ^$genotype_cond.genotype
-            #end if
-        #end if
-        #if str( $var_type_cond.set_var_type ) == "True":
-            #if str( $var_type_cond.include_or_exclude ) == "include":
-                --types $var_type_cond.var_types
-            #else
-                --exclude-types $var_type_cond.var_types
-            #end if
-        #end if
-        ${uncalled}
-        ${exclude_uncalled}
-        ${private}
-        ${exclude_private}
-
-        #if str( $input_file_index ) != "None":
-            input_file.${input.ext}
-        #else
-            $input
-        #end if
-    </command>
-
-    <inputs>
-        <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."/>
-        <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."/>
-        <param name="output_type" type="select" label="Output data type" help="-O">
-            <option value="v" selected="true">VCF</option>
-            <option value="b">BCF</option>
-        </param>
-        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="regions" type="text" size="20" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
-        <param name="targets" type="text" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
-            <sanitizer invalid_char="">
-                <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
-            </sanitizer>
-        </param>
-        <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
-        <param name="samples" type="text" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
-        <param name="apply_filters" type="text" optional="True" label="Apply filters" help="-f. Comma-separated list of strings. Keeps only sites where FILTER column contains one of these strings." />
-        <param name="drop_genotypes" type="boolean" checked="False" truevalue="--drop-genotypes" falsevalue="" label="Drop individual genotype information" help="-G" />
-        <param name="no_header" type="boolean" checked="False" truevalue="--no-header" falsevalue="" label="Suppress the header in VCF output" help="-H" />
-        <param name="header_only" type="boolean" checked="False" truevalue="--header-only" falsevalue="" label="Output the VCF header only" help="-h" />
-        <conditional name="min_ac_cond">
-            <param name="set_min_ac" type="boolean" checked="False" label="Set minimum allele count" help="-c" />
-            <when value="true">
-                <param name="min_ac" type="integer" optional="true" label="Minimum allele count" help="Minimum allele count of sites to be printed, for given allele type." />
-                <param name="min_ac_type" type="select" label="Allele type">
-                    <option value="nref" selected="True">Non-reference</option>
-                    <option value="alt1">1st alternate</option>
-                    <option value="minor">Minor (least frequent)</option>
-                    <option value="major">Major (most frequent)</option>
-                    <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
-                </param>
-            </when>
-        </conditional>
-        <conditional name="max_ac_cond">
-            <param name="set_max_ac" type="boolean" checked="False" label="Set maximum allele count" help="-C" />
-            <when value="true">
-                <param name="max_ac" type="integer" optional="true" label="Maximum allele count" help="Maximum allele count of sites to be printed, for given allele type." />
-                <param name="max_ac_type" type="select" label="Allele type">
-                    <option value="nref" selected="True">Non-reference</option>
-                    <option value="alt1">1st alternate</option>
-                    <option value="minor">Minor (least frequent)</option>
-                    <option value="major">Major (most frequent)</option>
-                    <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
-                </param>
-            </when>
-        </conditional>
-
-        <conditional name="min_af_cond">
-            <param name="set_min_af" type="boolean" checked="False" label="Set minimum allele frequency" help="-q" />
-            <when value="true">
-                <param name="min_af" type="integer" optional="true" label="Minimum allele frequency" help="Minimum allele frequency of sites to be printed, for given allele type." />
-                <param name="min_af_type" type="select" label="Allele type">
-                    <option value="nref" selected="True">Non-reference</option>
-                    <option value="alt1">1st alternate</option>
-                    <option value="minor">Minor (least frequent)</option>
-                    <option value="major">Major (most frequent)</option>
-                    <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
-                </param>
-            </when>
-        </conditional>
-        <conditional name="max_af_cond">
-            <param name="set_max_af" type="boolean" checked="False" label="Set maximum allele frequency" help="-Q" />
-            <when value="true">
-                <param name="max_af" type="integer" optional="true" label="Maximum allele frequency" help="Maximum allele frequency of sites to be printed, for given allele type." />
-                <param name="max_af_type" type="select" label="Allele type">
-                    <option value="nref" selected="True">Non-reference</option>
-                    <option value="alt1">1st alternate</option>
-                    <option value="minor">Minor (least frequent)</option>
-                    <option value="major">Major (most frequent)</option>
-                    <option value="nonmajor">Nonmajor (Sum of all but most frequent)</option>
-                </param>
-            </when>
-        </conditional>
-
-        <conditional name="genotype_cond">
-            <param name="set_genotype" type="boolean" checked="False" label="Filter by genotype" help="-g. Include only, or exclude, sites with one or more of given genotype."/>
-            <when value="true">
-                <param name="include_or_exclude" type="select" label="Include or exclude by genotype">
-                    <option value="include">Include</option>
-                    <option value="exclude">Exclude</option>
-                </param>
-                <param name="genotype" type="select" label="Genotype">
-                    <option value="hom">Homozygous</option>
-                    <option value="het">Heterozygous</option>
-                    <option value="miss">Missing</option>
-                </param>
-            </when>
-        </conditional>
-
-        <conditional name="expr_cond">
-            <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, -e. Include/ exclude sites for which expression is true. Must use valid expression."/>
-            <when value="true">
-                <param name="include_or_exclude" type="select" label="Include or exclude by expression">
-                    <option value="include">Include</option>
-                    <option value="exclude">Exclude</option>
-                </param>
-                <param name="expr" type="text" label="Expression">
-                    <sanitizer invalid_char="">
-                        <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
-                    </sanitizer>
-                </param>
-            </when>
-        </conditional>
-
-        <conditional name="var_type_cond">
-            <param name="set_var_type" type="boolean" checked="False" label="Filter by variant type" help="-v, -V. Include/ exclude sites where any ALT allele is one of the given variant types."/>
-            <when value="true">
-                <param name="include_or_exclude" type="select" label="Include or exclude by variant type">
-                    <option value="include">Include</option>
-                    <option value="exclude">Exclude</option>
-                </param>
-                <param name="var_types" type="select" multiple="true" display="checkboxes" label="Variant type">
-                    <option value="snps">SNPs</option>
-                    <option value="indels">Indels</option>
-                    <option value="mnps">MNPs</option>
-                    <option value="other">Other</option>
-                </param>
-            </when>
-        </conditional>
-
-        <param name="uncalled" type="boolean" checked="False" truevalue="--uncalled" falsevalue="" label="Print sites without a called genotype" help="-u" />
-        <param name="exclude_uncalled" type="boolean" checked="False" truevalue="--exclude-uncalled" falsevalue="" label="Exclude sites without a called genotype" help="-U" />
-        <param name="private" type="boolean" checked="False" truevalue="--private" falsevalue="" label="Print sites where only the subset samples carry a non-reference allele" help="-x. Requires samples file or samples list."/>
-        <param name="exclude_private" type="boolean" checked="False" truevalue="--exclude-private" falsevalue="" label="Exclude sites where only the subset samples carry a non-reference allele" help="-X. Requires samples file or samples list."/>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="output_type" value="b" format="bcf" />
-            </change_format>
-        </data>
-    </outputs>
-    <help>
-**About this tool**
-
-**BCFtools view**: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF. Former bcftools subset.
-
-Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
-  </help>
-</tool>
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