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5 <!DOCTYPE html>
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13 <title>galaxytools/samtools_sort.xml at master ยท bgruening/galaxytools</title>
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63 <body class="logged_in env-production macintosh vis-public page-blob">
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81 <form accept-charset="UTF-8" action="/bgruening/galaxytools/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/bgruening/galaxytools/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
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115 <span class="css-truncate-target">martenson</span>
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127
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128 <ul class="dropdown-menu">
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129 <li>
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130 <a href="/new"><span class="octicon octicon-repo"></span> New repository</a>
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131 </li>
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132 <li>
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133 <a href="/organizations/new"><span class="octicon octicon-organization"></span> New organization</a>
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139 <span title="bgruening/galaxytools">This repository</span>
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142 <a href="/bgruening/galaxytools/issues/new"><span class="octicon octicon-issue-opened"></span> New issue</a>
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143 </li>
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151 <span class="mail-status all-read"></span>
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152 <span class="octicon octicon-inbox"></span>
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153 </a>
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154 </li>
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155
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156 <li class="header-nav-item">
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157 <a class="header-nav-link tooltipped tooltipped-s" href="/settings/profile" id="account_settings" aria-label="Settings" data-ga-click="Header, go to settings, icon:settings">
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158 <span class="octicon octicon-gear"></span>
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159 </a>
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160 </li>
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161
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162 <li class="header-nav-item">
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163 <form accept-charset="UTF-8" action="/logout" class="logout-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="JmoHD8AuqFtwovPzUZGIZV+JkiupqKzpcox2nVexpunrzar6iFKMizQy6MEnyPU1gggJ28xGDE3tmZ5Vccn00g==" /></div>
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164 <button class="header-nav-link sign-out-button tooltipped tooltipped-s" aria-label="Sign out" data-ga-click="Header, sign out, icon:logout">
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165 <span class="octicon octicon-sign-out"></span>
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166 </button>
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167 </form> </li>
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168
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169 </ul>
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170
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171
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172
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173 </div>
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174 </div>
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175
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176
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177
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178
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179
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180
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181 <div id="start-of-content" class="accessibility-aid"></div>
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182 <div class="site" itemscope itemtype="http://schema.org/WebPage">
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183 <div id="js-flash-container">
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184
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185 </div>
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186 <div class="pagehead repohead instapaper_ignore readability-menu">
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187 <div class="container">
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188
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189 <ul class="pagehead-actions">
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190
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191 <li class="subscription">
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192 <form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="fMaqL7Kp35ooqsGLeroGbkRXZdvcR/Ud+D9LU+AoLA9v9NNB0RoFhGB+jF+UG/7CFaz7anex6nulIQ7dLj81mQ==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="6942323" />
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193
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194 <div class="select-menu js-menu-container js-select-menu">
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195 <a class="social-count js-social-count" href="/bgruening/galaxytools/watchers">
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196 18
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197 </a>
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198 <a href="/bgruening/galaxytools/subscription"
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199 class="minibutton select-menu-button with-count js-menu-target" role="button" tabindex="0" aria-haspopup="true">
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200 <span class="js-select-button">
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201 <span class="octicon octicon-eye"></span>
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202 Watch
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203 </span>
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204 </a>
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205
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206 <div class="select-menu-modal-holder">
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207 <div class="select-menu-modal subscription-menu-modal js-menu-content" aria-hidden="true">
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208 <div class="select-menu-header">
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209 <span class="select-menu-title">Notifications</span>
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210 <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
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211 </div> <!-- /.select-menu-header -->
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212
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213 <div class="select-menu-list js-navigation-container" role="menu">
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214
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215 <div class="select-menu-item js-navigation-item selected" role="menuitem" tabindex="0">
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216 <span class="select-menu-item-icon octicon octicon-check"></span>
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217 <div class="select-menu-item-text">
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218 <input checked="checked" id="do_included" name="do" type="radio" value="included" />
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219 <h4>Not watching</h4>
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220 <span class="description">Be notified when participating or @mentioned.</span>
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221 <span class="js-select-button-text hidden-select-button-text">
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222 <span class="octicon octicon-eye"></span>
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223 Watch
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224 </span>
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225 </div>
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226 </div> <!-- /.select-menu-item -->
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227
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228 <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
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229 <span class="select-menu-item-icon octicon octicon octicon-check"></span>
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230 <div class="select-menu-item-text">
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231 <input id="do_subscribed" name="do" type="radio" value="subscribed" />
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232 <h4>Watching</h4>
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233 <span class="description">Be notified of all conversations.</span>
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234 <span class="js-select-button-text hidden-select-button-text">
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235 <span class="octicon octicon-eye"></span>
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236 Unwatch
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237 </span>
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238 </div>
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239 </div> <!-- /.select-menu-item -->
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240
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241 <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
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242 <span class="select-menu-item-icon octicon octicon-check"></span>
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243 <div class="select-menu-item-text">
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244 <input id="do_ignore" name="do" type="radio" value="ignore" />
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245 <h4>Ignoring</h4>
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246 <span class="description">Never be notified.</span>
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247 <span class="js-select-button-text hidden-select-button-text">
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248 <span class="octicon octicon-mute"></span>
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249 Stop ignoring
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250 </span>
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251 </div>
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252 </div> <!-- /.select-menu-item -->
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253
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254 </div> <!-- /.select-menu-list -->
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255
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256 </div> <!-- /.select-menu-modal -->
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257 </div> <!-- /.select-menu-modal-holder -->
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258 </div> <!-- /.select-menu -->
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259
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260 </form>
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261 </li>
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262
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263 <li>
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264
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265 <div class="js-toggler-container js-social-container starring-container on">
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266
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267 <form accept-charset="UTF-8" action="/bgruening/galaxytools/unstar" class="js-toggler-form starred js-unstar-button" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="WdgMeXIjssImw51FieAml78d+6cYa/yjGiW4pnh85xdDzRTSsXfBdRUFyp7YPWk9E4Qk6UYawjSNJ1PH+IxnOg==" /></div>
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268 <button
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269 class="minibutton with-count js-toggler-target star-button"
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270 aria-label="Unstar this repository" title="Unstar bgruening/galaxytools">
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271 <span class="octicon octicon-star"></span>
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272 Unstar
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273 </button>
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274 <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers">
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275 20
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276 </a>
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277 </form>
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278 <form accept-charset="UTF-8" action="/bgruening/galaxytools/star" class="js-toggler-form unstarred js-star-button" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="p3NWhH6b56GUJWoobNdalnehY7EfoKfOxt7yTeqNsweU2MXvu0HUFbklxPN23kuCJwxPj+nCwsW/CoBmKErn6Q==" /></div>
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279 <button
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280 class="minibutton with-count js-toggler-target star-button"
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281 aria-label="Star this repository" title="Star bgruening/galaxytools">
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282 <span class="octicon octicon-star"></span>
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283 Star
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284 </button>
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285 <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers">
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286 20
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287 </a>
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288 </form> </div>
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289
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290 </li>
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291
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292
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293 <li>
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294 <a href="/bgruening/galaxytools/fork" class="minibutton with-count js-toggler-target fork-button tooltipped-n" title="Fork your own copy of bgruening/galaxytools to your account" aria-label="Fork your own copy of bgruening/galaxytools to your account" rel="nofollow" data-method="post">
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295 <span class="octicon octicon-repo-forked"></span>
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296 Fork
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297 </a>
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298 <a href="/bgruening/galaxytools/network" class="social-count">22</a>
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299 </li>
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300
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301 </ul>
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302
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303 <h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public">
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304 <span class="mega-octicon octicon-repo"></span>
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305 <span class="author"><a href="/bgruening" class="url fn" itemprop="url" rel="author"><span itemprop="title">bgruening</span></a></span><!--
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306 --><span class="path-divider">/</span><!--
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307 --><strong><a href="/bgruening/galaxytools" class="js-current-repository js-repo-home-link">galaxytools</a></strong>
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308
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309 <span class="page-context-loader">
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310 <img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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311 </span>
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312
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313 </h1>
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314 </div><!-- /.container -->
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315 </div><!-- /.repohead -->
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316
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317 <div class="container">
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318 <div class="repository-with-sidebar repo-container new-discussion-timeline ">
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319 <div class="repository-sidebar clearfix">
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320
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321 <div class="sunken-menu vertical-right repo-nav js-repo-nav js-repository-container-pjax js-octicon-loaders" data-issue-count-url="/bgruening/galaxytools/issues/counts">
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322 <div class="sunken-menu-contents">
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323 <ul class="sunken-menu-group">
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324 <li class="tooltipped tooltipped-w" aria-label="Code">
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325 <a href="/bgruening/galaxytools" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-pjax="true" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /bgruening/galaxytools">
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326 <span class="octicon octicon-code"></span> <span class="full-word">Code</span>
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327 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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328 </a> </li>
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329
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330 <li class="tooltipped tooltipped-w" aria-label="Issues">
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331 <a href="/bgruening/galaxytools/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /bgruening/galaxytools/issues">
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332 <span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
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333 <span class="js-issue-replace-counter"></span>
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334 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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335 </a> </li>
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336
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337 <li class="tooltipped tooltipped-w" aria-label="Pull Requests">
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338 <a href="/bgruening/galaxytools/pulls" aria-label="Pull Requests" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g p" data-selected-links="repo_pulls /bgruening/galaxytools/pulls">
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339 <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull Requests</span>
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340 <span class="js-pull-replace-counter"></span>
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341 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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342 </a> </li>
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343
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344
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345 <li class="tooltipped tooltipped-w" aria-label="Wiki">
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346 <a href="/bgruening/galaxytools/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g w" data-selected-links="repo_wiki /bgruening/galaxytools/wiki">
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347 <span class="octicon octicon-book"></span> <span class="full-word">Wiki</span>
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348 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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349 </a> </li>
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350 </ul>
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351 <div class="sunken-menu-separator"></div>
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352 <ul class="sunken-menu-group">
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353
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354 <li class="tooltipped tooltipped-w" aria-label="Pulse">
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355 <a href="/bgruening/galaxytools/pulse/weekly" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="pulse /bgruening/galaxytools/pulse/weekly">
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356 <span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
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357 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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358 </a> </li>
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359
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360 <li class="tooltipped tooltipped-w" aria-label="Graphs">
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361 <a href="/bgruening/galaxytools/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="repo_graphs repo_contributors /bgruening/galaxytools/graphs">
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362 <span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span>
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363 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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364 </a> </li>
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365 </ul>
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366
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367
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368 </div>
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369 </div>
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370
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371 <div class="only-with-full-nav">
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372
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373
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374 <div class="clone-url open"
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375 data-protocol-type="http"
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376 data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone">
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377 <h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
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378 <div class="input-group">
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379 <input type="text" class="input-mini input-monospace js-url-field"
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380 value="https://github.com/bgruening/galaxytools.git" readonly="readonly">
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381 <span class="input-group-button">
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382 <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
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383 </span>
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384 </div>
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385 </div>
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386
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387
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388 <div class="clone-url "
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389 data-protocol-type="ssh"
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390 data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone">
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391 <h3><span class="text-emphasized">SSH</span> clone URL</h3>
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392 <div class="input-group">
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393 <input type="text" class="input-mini input-monospace js-url-field"
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394 value="git@github.com:bgruening/galaxytools.git" readonly="readonly">
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395 <span class="input-group-button">
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396 <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="git@github.com:bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
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397 </span>
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398 </div>
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399 </div>
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400
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401
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402 <div class="clone-url "
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403 data-protocol-type="subversion"
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404 data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone">
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405 <h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
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406 <div class="input-group">
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407 <input type="text" class="input-mini input-monospace js-url-field"
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408 value="https://github.com/bgruening/galaxytools" readonly="readonly">
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409 <span class="input-group-button">
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410 <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
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411 </span>
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412 </div>
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413 </div>
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414
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415
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416 <p class="clone-options">You can clone with
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417 <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a>,
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418 <a href="#" class="js-clone-selector" data-protocol="ssh">SSH</a>,
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419 or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>.
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420 <a href="https://help.github.com/articles/which-remote-url-should-i-use" class="help tooltipped tooltipped-n" aria-label="Get help on which URL is right for you.">
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421 <span class="octicon octicon-question"></span>
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422 </a>
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423 </p>
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424
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425 <a href="http://mac.github.com" data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools" class="minibutton sidebar-button js-conduit-rewrite-url" title="Save bgruening/galaxytools to your computer and use it in GitHub Desktop." aria-label="Save bgruening/galaxytools to your computer and use it in GitHub Desktop.">
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426 <span class="octicon octicon-device-desktop"></span>
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427 Clone in Desktop
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428 </a>
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429
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430
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431 <a href="/bgruening/galaxytools/archive/master.zip"
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432 class="minibutton sidebar-button"
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433 aria-label="Download the contents of bgruening/galaxytools as a zip file"
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434 title="Download the contents of bgruening/galaxytools as a zip file"
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435 rel="nofollow">
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436 <span class="octicon octicon-cloud-download"></span>
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437 Download ZIP
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438 </a>
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439 </div>
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440 </div><!-- /.repository-sidebar -->
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441
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442 <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container>
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443
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444
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445 <a href="/bgruening/galaxytools/blob/3a57ada6062aa513010b1bc15048135d4207f337/samtools_sort/samtools_sort.xml" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a>
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446
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447 <!-- blob contrib key: blob_contributors:v21:f40ff95d19e5c54ca033554fe611f373 -->
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448
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449 <div class="file-navigation">
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450
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451 <div class="select-menu js-menu-container js-select-menu left">
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452 <span class="minibutton select-menu-button js-menu-target css-truncate" data-hotkey="w"
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453 data-master-branch="master"
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454 data-ref="master"
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455 title="master"
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456 role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true">
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457 <span class="octicon octicon-git-branch"></span>
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458 <i>branch:</i>
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459 <span class="js-select-button css-truncate-target">master</span>
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460 </span>
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461
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462 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true">
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463
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464 <div class="select-menu-modal">
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465 <div class="select-menu-header">
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466 <span class="select-menu-title">Switch branches/tags</span>
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467 <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
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468 </div> <!-- /.select-menu-header -->
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469
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470 <div class="select-menu-filters">
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471 <div class="select-menu-text-filter">
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472 <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
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473 </div>
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474 <div class="select-menu-tabs">
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475 <ul>
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476 <li class="select-menu-tab">
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477 <a href="#" data-tab-filter="branches" class="js-select-menu-tab">Branches</a>
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478 </li>
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479 <li class="select-menu-tab">
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480 <a href="#" data-tab-filter="tags" class="js-select-menu-tab">Tags</a>
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481 </li>
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482 </ul>
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483 </div><!-- /.select-menu-tabs -->
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484 </div><!-- /.select-menu-filters -->
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485
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486 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches">
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487
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488 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
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489
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490
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491 <div class="select-menu-item js-navigation-item ">
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492 <span class="select-menu-item-icon octicon octicon-check"></span>
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493 <a href="/bgruening/galaxytools/blob/gh-pages/samtools_sort/samtools_sort.xml"
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494 data-name="gh-pages"
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495 data-skip-pjax="true"
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498 title="gh-pages">gh-pages</a>
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499 </div> <!-- /.select-menu-item -->
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500 <div class="select-menu-item js-navigation-item selected">
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501 <span class="select-menu-item-icon octicon octicon-check"></span>
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502 <a href="/bgruening/galaxytools/blob/master/samtools_sort/samtools_sort.xml"
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503 data-name="master"
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504 data-skip-pjax="true"
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505 rel="nofollow"
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506 class="js-navigation-open select-menu-item-text css-truncate-target"
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507 title="master">master</a>
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508 </div> <!-- /.select-menu-item -->
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509 </div>
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510
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511 <div class="select-menu-no-results">Nothing to show</div>
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513
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514 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags">
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515 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
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516
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517
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518 </div>
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519
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520 <div class="select-menu-no-results">Nothing to show</div>
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521 </div> <!-- /.select-menu-list -->
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522
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523 </div> <!-- /.select-menu-modal -->
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524 </div> <!-- /.select-menu-modal-holder -->
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525 </div> <!-- /.select-menu -->
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526
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527 <div class="button-group right">
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528 <a href="/bgruening/galaxytools/find/master"
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529 class="js-show-file-finder minibutton empty-icon tooltipped tooltipped-s"
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530 data-pjax
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531 data-hotkey="t"
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532 aria-label="Quickly jump between files">
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533 <span class="octicon octicon-list-unordered"></span>
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534 </a>
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535 <button class="js-zeroclipboard minibutton zeroclipboard-button"
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536 data-clipboard-text="samtools_sort/samtools_sort.xml"
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537 aria-label="Copy to clipboard"
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538 data-copied-hint="Copied!">
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539 <span class="octicon octicon-clippy"></span>
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540 </button>
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541 </div>
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542
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543 <div class="breadcrumb">
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544 <span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">galaxytools</span></a></span></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">samtools_sort</span></a></span><span class="separator"> / </span><strong class="final-path">samtools_sort.xml</strong>
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545 </div>
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546 </div>
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547
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548
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549 <div class="commit file-history-tease">
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550 <div class="file-history-tease-header">
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551 <img alt="Bjรถrn Grรผning" class="avatar" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" />
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552 <span class="author"><a href="/bgruening" rel="author">bgruening</a></span>
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553 <time datetime="2014-06-23T10:59:43+02:00" is="relative-time">June 23, 2014</time>
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554 <div class="commit-title">
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555 <a href="/bgruening/galaxytools/commit/3314eedb2e44d2c4b481c1f274ac27e03b8760c5" class="message" data-pjax="true" title="add new test data">add new test data</a>
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556 </div>
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557 </div>
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558
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559 <div class="participation">
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560 <p class="quickstat">
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561 <a href="#blob_contributors_box" rel="facebox">
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562 <strong>1</strong>
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563 contributor
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564 </a>
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565 </p>
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566
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567 </div>
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568 <div id="blob_contributors_box" style="display:none">
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569 <h2 class="facebox-header">Users who have contributed to this file</h2>
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570 <ul class="facebox-user-list">
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571 <li class="facebox-user-list-item">
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572 <img alt="Bjรถrn Grรผning" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" />
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573 <a href="/bgruening">bgruening</a>
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574 </li>
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575 </ul>
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576 </div>
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577 </div>
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578
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579 <div class="file-box">
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580 <div class="file">
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581 <div class="meta clearfix">
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582 <div class="info file-name">
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583 <span>48 lines (39 sloc)</span>
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584 <span class="meta-divider"></span>
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585 <span>1.653 kb</span>
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586 </div>
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587 <div class="actions">
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588 <div class="button-group">
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589 <a href="/bgruening/galaxytools/raw/master/samtools_sort/samtools_sort.xml" class="minibutton " id="raw-url">Raw</a>
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590 <a href="/bgruening/galaxytools/blame/master/samtools_sort/samtools_sort.xml" class="minibutton js-update-url-with-hash">Blame</a>
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591 <a href="/bgruening/galaxytools/commits/master/samtools_sort/samtools_sort.xml" class="minibutton " rel="nofollow">History</a>
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592 </div><!-- /.button-group -->
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593
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594 <a class="octicon-button tooltipped tooltipped-nw js-conduit-openfile-check"
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595 href="http://mac.github.com"
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596 data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools?branch=master&filepath=samtools_sort%2Fsamtools_sort.xml"
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597 aria-label="Open this file in GitHub for Mac"
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598 data-failed-title="Your version of GitHub for Mac is too old to open this file. Try checking for updates.">
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599 <span class="octicon octicon-device-desktop"></span>
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600 </a>
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601
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602 <a class="octicon-button tooltipped tooltipped-n js-update-url-with-hash"
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603 aria-label="Clicking this button will fork this project so you can edit the file"
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604 href="/bgruening/galaxytools/edit/master/samtools_sort/samtools_sort.xml"
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605 data-method="post" rel="nofollow"><span class="octicon octicon-pencil"></span></a>
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606
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607 <a class="octicon-button danger tooltipped tooltipped-s"
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608 href="/bgruening/galaxytools/delete/master/samtools_sort/samtools_sort.xml"
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609 aria-label="Fork this project and delete file"
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610 data-method="post" data-test-id="delete-blob-file" rel="nofollow">
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611 <span class="octicon octicon-trashcan"></span>
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612 </a>
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613 </div><!-- /.actions -->
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614 </div>
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615
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616 <div class="blob-wrapper data type-xml">
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617 <table class="highlight tab-size-8 js-file-line-container">
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618 <tr>
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619 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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620 <td id="LC1" class="blob-code js-file-line"><span class="nt"><tool</span> <span class="na">id=</span><span class="s">"samtools_sort"</span> <span class="na">name=</span><span class="s">"sort"</span> <span class="na">version=</span><span class="s">"1.0.2"</span><span class="nt">></span></td>
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621 </tr>
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622 <tr>
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623 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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624 <td id="LC2" class="blob-code js-file-line"> <span class="nt"><requirements></span></td>
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625 </tr>
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626 <tr>
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627 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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628 <td id="LC3" class="blob-code js-file-line"> <span class="nt"><requirement</span> <span class="na">type=</span><span class="s">"package"</span> <span class="na">version=</span><span class="s">"0.1.19"</span><span class="nt">></span>samtools<span class="nt"></requirement></span></td>
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629 </tr>
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630 <tr>
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631 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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632 <td id="LC4" class="blob-code js-file-line"> <span class="nt"></requirements></span></td>
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633 </tr>
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634 <tr>
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635 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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636 <td id="LC5" class="blob-code js-file-line"> <span class="nt"><description></span>a BAM file<span class="nt"></description></span></td>
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637 </tr>
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638 <tr>
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639 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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640 <td id="LC6" class="blob-code js-file-line"> <span class="nt"><command></span></td>
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641 </tr>
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642 <tr>
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643 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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644 <td id="LC7" class="blob-code js-file-line"> samtools sort</td>
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645 </tr>
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646 <tr>
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647 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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648 <td id="LC8" class="blob-code js-file-line"> $sort_mode</td>
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649 </tr>
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650 <tr>
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651 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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652 <td id="LC9" class="blob-code js-file-line"> "${input1}" foo</td>
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653 </tr>
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654 <tr>
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655 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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656 <td id="LC10" class="blob-code js-file-line"> 2<span class="ni">&gt;&amp;</span>1 || echo "Error running samtools sort." <span class="ni">&gt;&amp;</span>2</td>
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657 </tr>
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658 <tr>
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659 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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660 <td id="LC11" class="blob-code js-file-line"> ;</td>
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661 </tr>
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662 <tr>
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663 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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664 <td id="LC12" class="blob-code js-file-line"> mv foo.bam "${output1}"</td>
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665 </tr>
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666 <tr>
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667 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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668 <td id="LC13" class="blob-code js-file-line"> <span class="nt"></command></span></td>
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669 </tr>
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670 <tr>
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671 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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672 <td id="LC14" class="blob-code js-file-line"> <span class="nt"><inputs></span></td>
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673 </tr>
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674 <tr>
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675 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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676 <td id="LC15" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"input1"</span> <span class="na">type=</span><span class="s">"data"</span> <span class="na">format=</span><span class="s">"bam"</span> <span class="na">label=</span><span class="s">"BAM File"</span> <span class="nt">/></span></td>
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677 </tr>
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678 <tr>
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679 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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680 <td id="LC16" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"sort_mode"</span> <span class="na">type=</span><span class="s">"select"</span> <span class="na">label=</span><span class="s">"Sort by "</span><span class="nt">></span></td>
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681 </tr>
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682 <tr>
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683 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
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684 <td id="LC17" class="blob-code js-file-line"> <span class="nt"><option</span> <span class="na">value=</span><span class="s">""</span> <span class="na">selected=</span><span class="s">"True"</span><span class="nt">></span>Chromosomal coordinates<span class="nt"></option></span></td>
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685 </tr>
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686 <tr>
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687 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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688 <td id="LC18" class="blob-code js-file-line"> <span class="nt"><option</span> <span class="na">value=</span><span class="s">"-n"</span><span class="nt">></span>Read names<span class="nt"></option></span></td>
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689 </tr>
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690 <tr>
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691 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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692 <td id="LC19" class="blob-code js-file-line"> <span class="nt"></param></span></td>
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693 </tr>
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694 <tr>
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695 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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696 <td id="LC20" class="blob-code js-file-line"> <span class="nt"></inputs></span></td>
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697 </tr>
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698 <tr>
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699 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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700 <td id="LC21" class="blob-code js-file-line"> <span class="nt"><outputs></span></td>
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701 </tr>
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702 <tr>
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703 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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704 <td id="LC22" class="blob-code js-file-line"> <span class="nt"><data</span> <span class="na">name=</span><span class="s">"output1"</span> <span class="na">format=</span><span class="s">"bam"</span> <span class="nt">/></span></td>
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705 </tr>
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706 <tr>
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707 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
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708 <td id="LC23" class="blob-code js-file-line"> <span class="nt"></outputs></span></td>
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709 </tr>
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710 <tr>
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711 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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712 <td id="LC24" class="blob-code js-file-line"> <span class="nt"><tests></span></td>
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713 </tr>
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714 <tr>
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715 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
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716 <td id="LC25" class="blob-code js-file-line"> <span class="nt"><test></span></td>
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717 </tr>
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718 <tr>
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719 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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720 <td id="LC26" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"input1"</span> <span class="na">value=</span><span class="s">"1.bam"</span> <span class="na">ftype=</span><span class="s">"bam"</span> <span class="nt">/></span></td>
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721 </tr>
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722 <tr>
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723 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
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724 <td id="LC27" class="blob-code js-file-line"> <span class="nt"><output</span> <span class="na">name=</span><span class="s">"output1"</span> <span class="na">file=</span><span class="s">"1_sort.bam"</span> <span class="na">ftype=</span><span class="s">"bam"</span> <span class="na">sort=</span><span class="s">"True"</span><span class="nt">/></span></td>
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725 </tr>
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726 <tr>
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727 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
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728 <td id="LC28" class="blob-code js-file-line"> <span class="nt"></test></span></td>
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729 </tr>
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730 <tr>
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731 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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732 <td id="LC29" class="blob-code js-file-line"> <span class="nt"></tests></span></td>
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733 </tr>
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734 <tr>
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735 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
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736 <td id="LC30" class="blob-code js-file-line"> <span class="nt"><help></span></td>
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737 </tr>
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738 <tr>
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739 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
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740 <td id="LC31" class="blob-code js-file-line">
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741 </td>
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742 </tr>
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743 <tr>
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744 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
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745 <td id="LC32" class="blob-code js-file-line">**What it does**</td>
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746 </tr>
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747 <tr>
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748 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
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749 <td id="LC33" class="blob-code js-file-line">
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750 </td>
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751 </tr>
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752 <tr>
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753 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
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754 <td id="LC34" class="blob-code js-file-line">This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.</td>
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755 </tr>
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756 <tr>
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757 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
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758 <td id="LC35" class="blob-code js-file-line">
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759 </td>
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760 </tr>
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761 <tr>
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762 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
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763 <td id="LC36" class="blob-code js-file-line">.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml</td>
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764 </tr>
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765 <tr>
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766 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
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767 <td id="LC37" class="blob-code js-file-line">
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768 </td>
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769 </tr>
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770 <tr>
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771 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
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772 <td id="LC38" class="blob-code js-file-line">------</td>
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773 </tr>
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774 <tr>
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775 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
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776 <td id="LC39" class="blob-code js-file-line">
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777 </td>
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778 </tr>
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779 <tr>
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780 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
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781 <td id="LC40" class="blob-code js-file-line">**Citation**</td>
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782 </tr>
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783 <tr>
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784 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
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785 <td id="LC41" class="blob-code js-file-line">
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786 </td>
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787 </tr>
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788 <tr>
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789 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
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|
790 <td id="LC42" class="blob-code js-file-line">For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <span class="ni">&lt;</span>http://www.ncbi.nlm.nih.gov/pubmed/19505943<span class="ni">&gt;</span>`_</td>
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791 </tr>
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792 <tr>
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793 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
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794 <td id="LC43" class="blob-code js-file-line">
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795 </td>
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796 </tr>
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797 <tr>
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798 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
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799 <td id="LC44" class="blob-code js-file-line">If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*</td>
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800 </tr>
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801 <tr>
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802 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
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803 <td id="LC45" class="blob-code js-file-line">
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804 </td>
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805 </tr>
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806 <tr>
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807 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
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808 <td id="LC46" class="blob-code js-file-line"> <span class="nt"></help></span></td>
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|
809 </tr>
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|
810 <tr>
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|
811 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
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|
812 <td id="LC47" class="blob-code js-file-line"><span class="nt"></tool></span></td>
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813 </tr>
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|
814 </table>
|
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815
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816 </div>
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817
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818 </div>
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819 </div>
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820
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821 <a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a>
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822 <div id="jump-to-line" style="display:none">
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823 <form accept-charset="UTF-8" class="js-jump-to-line-form">
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824 <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus>
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825 <button type="submit" class="button">Go</button>
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826 </form>
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827 </div>
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828
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829 </div>
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830
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831 </div><!-- /.repo-container -->
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832 <div class="modal-backdrop"></div>
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833 </div><!-- /.container -->
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834 </div><!-- /.site -->
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835
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838
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840 <div class="site-footer">
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841 <ul class="site-footer-links right">
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842 <li><a href="https://status.github.com/">Status</a></li>
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843 <li><a href="http://developer.github.com">API</a></li>
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844 <li><a href="http://training.github.com">Training</a></li>
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845 <li><a href="http://shop.github.com">Shop</a></li>
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846 <li><a href="/blog">Blog</a></li>
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847 <li><a href="/about">About</a></li>
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848
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850
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851 <a href="/" aria-label="Homepage">
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852 <span class="mega-octicon octicon-mark-github" title="GitHub"></span>
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853 </a>
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854
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855 <ul class="site-footer-links">
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856 <li>© 2014 <span title="0.04104s from github-fe135-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
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857 <li><a href="/site/terms">Terms</a></li>
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858 <li><a href="/site/privacy">Privacy</a></li>
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859 <li><a href="/security">Security</a></li>
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860 <li><a href="/contact">Contact</a></li>
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861 </ul>
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862 </div><!-- /.site-footer -->
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863 </div><!-- /.container -->
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864
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866 <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay">
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867 <div class="fullscreen-container js-suggester-container">
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868 <div class="textarea-wrap">
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869 <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents js-suggester-field" placeholder=""></textarea>
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870 </div>
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872 <div class="fullscreen-sidebar">
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873 <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode">
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874 <span class="mega-octicon octicon-screen-normal"></span>
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875 </a>
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876 <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w"
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877 aria-label="Switch themes">
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878 <span class="octicon octicon-color-mode"></span>
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879 </a>
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880 </div>
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881 </div>
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882
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883
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884
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885 <div id="ajax-error-message" class="flash flash-error">
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886 <span class="octicon octicon-alert"></span>
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887 <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a>
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888 Something went wrong with that request. Please try again.
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889 </div>
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890
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891
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892 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-0c1b00f7935ae85624f5fc5d40d52d60febf92b4.js" type="text/javascript"></script>
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893 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-cbba41b870c9e4d89d40771e5c675b37b14e9601.js" type="text/javascript"></script>
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894
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895
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896 <script async src="https://www.google-analytics.com/analytics.js"></script>
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897 </body>
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898 </html>
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899
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