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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="zlib" version="1.2.8">
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4 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bcftools" version="1.2">
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7 <install version="1.0">
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8 <actions_group>
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9 <!--actions os="linux" architecture="x86_64">
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10 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bcftools/bcftools-1.2-Linux-x86_64.tgz</action>
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11 <action type="move_directory_files">
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12 <source_directory>.</source_directory>
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13 <destination_directory>$INSTALL_DIR</destination_directory>
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14 </action>
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15 </actions-->
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16 <actions>
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17 <action type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2</action>
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18 <action type="set_environment_for_install">
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19 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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20 <package name="zlib" version="1.2.8" />
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21 </repository>
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22 </action>
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23 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
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24 <action type="shell_command">make</action>
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25 <action type="move_file">
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26 <source>bcftools</source>
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27 <destination>$INSTALL_DIR/bin</destination>
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28 </action>
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29 </actions>
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30 <action type="set_environment">
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31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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32 <environment_variable action="set_to" name="BCFTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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33 </action>
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34 </actions_group>
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35 </install>
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36 <readme>
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37 Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
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38 Version: 1.2 (using htslib 1.2.1)
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39
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40 Usage: bcftools <command> <argument>
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41
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42 Commands:
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43
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44 -- Indexing
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45 index index VCF/BCF files
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46
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47 -- VCF/BCF manipulation
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48 annotate annotate and edit VCF/BCF files
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49 concat concatenate VCF/BCF files from the same set of samples
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50 convert convert VCF/BCF files to different formats and back
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51 isec intersections of VCF/BCF files
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52 merge merge VCF/BCF files files from non-overlapping sample sets
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53 norm left-align and normalize indels
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54 plugin user-defined plugins
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55 query transform VCF/BCF into user-defined formats
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56 reheader modify VCF/BCF header, change sample names
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57 view VCF/BCF conversion, view, subset and filter VCF/BCF files
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58
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59 -- VCF/BCF analysis
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60 call SNP/indel calling
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61 consensus create consensus sequence by applying VCF variants
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62 filter filter VCF/BCF files using fixed thresholds
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63 gtcheck check sample concordance, detect sample swaps and contamination
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64 roh identify runs of autozygosity (HMM)
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65 stats produce VCF/BCF stats
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66
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67 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
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68 automatically even when streaming from a pipe. Indexed VCF and BCF will work
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69 in all situations. Un-indexed VCF and BCF and streams will work in most but
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70 not all situations.
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71
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72 </readme>
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73 </package>
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74 </tool_dependency>
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