stacks_clonefilter: macros.xml annotate

annotate macros.xml @ 0:a8a0cd05d47d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439

author	iuc
date	Sun, 21 May 2017 18:54:11 -0400
parents
children	5d12a1115770

rev	line source
0 a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	1 <?xml version="1.0"?>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	2 <macros>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	3 <xml name="requirements">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	4 <requirements>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	5 <requirement type="package" version="1.46">stacks</requirement>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	6 <requirement type="package" version="1.2.10">velvet</requirement>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	7 <requirement type="package" version="1.1">stacks_summary</requirement>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	8 <yield/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	9 </requirements>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	10 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	11
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	12 <token name="@WRAPPER_VERSION@">1.46</token>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	13
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	14 <xml name="stdio">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	15 <stdio>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	16 <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	17 </stdio>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	18 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	19
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	20 <xml name="citation">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	21 <citations>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	22 <citation type="doi">10.1111/mec.12354</citation>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	23 <citation type="doi">10.1111/mec.12330</citation>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	24 <citation type="doi">10.1534/g3.111.000240</citation>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	25 <citation type="doi">10.1534/genetics.111.127324</citation>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	26 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	27 <citation type="doi">10.1073/pnas.1006538107</citation>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	28 </citations>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	29 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	30
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	31 <token name="@STACKS_INFOS@">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	32 <![CDATA[
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	33 --------
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	34
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	35 Created by:
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	36
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	37 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	38
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	39 Project links:
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	40
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	41 `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	42
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	43 `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	44
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	45 `Stacks google group <http://groups.google.com/group/stacks-users>`_
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	46 ]]></token>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	47
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	48 <xml name="enzymes">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	49 <option value="aciI">aciI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	50 <option value="ageI">ageI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	51 <option value="aluI">aluI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	52 <option value="apeKI">apeKI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	53 <option value="apoI">apoI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	54 <option value="aseI">aseI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	55 <option value="bamHI">bamHI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	56 <option value="bfaI">bfaI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	57 <option value="bgIII">bgIII</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	58 <option value="bspDI">bspDI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	59 <option value="bstYI">bstYI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	60 <option value="claI">claI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	61 <option value="ddeI">ddeI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	62 <option value="dpnII">dpnII</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	63 <option value="eaeI">eaeI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	64 <option value="ecoRI">ecoRI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	65 <option value="ecoRV">ecoRV</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	66 <option value="ecoT22I">ecoT22I</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	67 <option value="hindIII">hindIII</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	68 <option value="kpnI">kpnI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	69 <option value="mluCI">mluCI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	70 <option value="mseI">mseI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	71 <option value="mspI">mspI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	72 <option value="ndeI">ndeI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	73 <option value="nheI">nheI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	74 <option value="nlaIII">nlaIII</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	75 <option value="notI">notI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	76 <option value="nsiI">nsiI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	77 <option value="pstI">pstI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	78 <option value="rsaI">rsaI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	79 <option value="sacI">sacI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	80 <option value="sau3AI">sau3AI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	81 <option value="sbfI">sbfI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	82 <option value="sexAI">sexAI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	83 <option value="sgrAI">sgrAI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	84 <option value="speI">speI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	85 <option value="sphI">sphI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	86 <option value="taqI">taqI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	87 <option value="xbaI">xbaI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	88 <option value="xhoI">xhoI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	89 <option value="csp6I">csp6I</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	90 <option value="bsaHI">bsaHI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	91 <option value="hpaII">hpaII</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	92 <option value="ncoI">ncoI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	93 <option value="ApaLI">ApaLI</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	94 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	95
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	96 <xml name="cross_types">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	97 <option value="CP">CP (F1 cross)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	98 <option value="F2">F2 (F2 cross)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	99 <option value="BC1">BC1 (backcross)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	100 <option value="DH">DH (double haploid cross)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	101 <option value="GEN">GEN (generic, unspecific to any map type)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	102 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	103
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	104 <token name="@CLEAN_EXT@">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	105 <![CDATA[
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	106 #from os.path import splitext
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	107 #import re
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	108 #def clean_ext($identifier)
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	109 #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	110 #set $identifier = splitext($identifier)[0]
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	111 #end while
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	112 $identifier#slurp
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	113 #end def
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	114 ]]>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	115 </token>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	116
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	117 <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	118 <![CDATA[
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	119 ## We need to do this as the output file names contains the value of an option (min progeny)
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	120 &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	121 cd stacks_outputs/ &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	122 ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	123 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	124 ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	125 ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	126 cd ..
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	127 ]]>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	128 </token>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	129
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	130 <token name="@NORM_GENOTYPES_OUTPUT_FULL@">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	131 <![CDATA[
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	132 ## We need to do this as the output file names contains the value of an option (min progeny)
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	133 &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	134 cd stacks_outputs/ &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	135 ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	136 ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	137 ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	138 ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	139 ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	140 ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	141 ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	142 ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	143 cd ..
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	144 ]]>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	145 </token>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	146
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	147 <xml name="genotypes_output_light">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	148
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	149 <data format="txt" name="out_joinmap" label="Haplotypes table (JoinMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.loc">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	150 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	151 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	152 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	153
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	154 <data format="tabular" name="out_generic_haplo" label="Haplotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	155 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	156 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	157 <data format="tabular" name="out_generic_geno" label="Genotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	158 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	159 <filter>options_usage['cross_type'] == "GEN"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	160 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	161
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	162 <data format="tabular" name="out_sql_markers" label="Markers table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	163 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	164 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	165
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	166 <data format="tabular" name="out_sql_genotypes" label="Haplotypes table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.txt">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	167 <filter>options_usage['rad_analysis_type'] == "genetic"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	168 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	169 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	170
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	171 <xml name="genotypes_output_full">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	172 <!-- Output formats generated by genotypes:
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	173
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	174 JoinMap, default, only if map type is F2/BC1/DH/CP => batch_1.genotypes_1.loc
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	175 OneMap, only if map type is F2/BC1 => batch_1.genotypes_1onemap.tsv
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	176 OneMap/MapMaker, only if map type is CP => batch_1.genotypes_1.onemap.txt
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	177 Genomic, for all map types => batch_1.genomic_1.tsv
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	178 R/QTL, only if map type is F2/BC1/DH => batch_1.genotypes_1.rqtl.tsv
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	179
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	180 Additional non-optional output (ie not altered by -o option):
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	181
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	182 Generic format, for every map types => batch_1.haplotypes_1.tsv
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	183 Generic format, if map type is GEN => batch_1.genotypes_1.tsv -->
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	184
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	185 <data format="txt" name="out_joinmap" label="Haplotypes table (JoinMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.loc">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	186 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH', 'CP']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	187 <filter>'map_out' not in options_usage or options_usage['map_out']['map_out_type'] == 'joinmap'</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	188 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	189
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	190 <data format="tabular" name="out_onemap" label="Haplotypes table (OneMap format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.onemap.txt">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	191 <filter>options_usage['cross_type'] in ['F2', 'BC1']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	192 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	193 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	194
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	195 <data format="tabular" name="out_onemap_mapmaker" label="Haplotypes table (OneMap/MapMaker format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.onemap.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	196 <filter>options_usage['cross_type'] in ['CP']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	197 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'onemap'</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	198 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	199
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	200 <data format="tabular" name="out_genomic" label="Haplotypes table (Genomic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genomic.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	201 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'genomic'</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	202 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	203
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	204 <data format="tabular" name="out_rqtl" label="Haplotypes table (R/QTL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.rqtl.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	205 <filter>options_usage['cross_type'] in ['F2', 'BC1', 'DH']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	206 <filter>'map_out' in options_usage and options_usage['map_out']['map_out_type'] == 'rqtl'</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	207 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	208
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	209 <data format="tabular" name="out_generic_haplo" label="Haplotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	210
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	211 <data format="tabular" name="out_generic_geno" label="Genotypes table (generic format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	212 <filter>options_usage['cross_type'] == "GEN"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	213 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	214
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	215 <data format="tabular" name="out_sql_markers" label="Markers table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	216
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	217 <data format="tabular" name="out_sql_genotypes" label="Haplotypes table (Stacks SQL format) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genotypes.txt"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	218 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	219
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	220 <xml name="populations_output_light">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	221 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	222 <filter>options_usage['rad_analysis_type'] == "population"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	223 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	224
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	225 <data format="tabular" name="out_hapstats" label="Haplotype-based summary statistics for each locus in each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hapstats.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	226 <filter>options_usage['rad_analysis_type'] == "population"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	227 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	228
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	229 <data format="tabular" name="out_populations_log" label="Populations log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.populations.log">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	230 <filter>options_usage['rad_analysis_type'] == "population"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	231 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	232
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	233 <data format="tabular" name="out_sumstats_sum" label="Summary of summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats_summary.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	234 <filter>options_usage['rad_analysis_type'] == "population"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	235 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	236
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	237 <data format="tabular" name="out_sumstats" label="Summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	238 <filter>options_usage['rad_analysis_type'] == "population"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	239 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	240
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	241 <data format="tabular" name="out_sql" label="Stacks SQL format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	242 <filter>options_usage['rad_analysis_type'] == "population"</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	243 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	244 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	245
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	246 <xml name="populations_output_full">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	247 <data format="tabular" name="out_haplotypes" label="Observed haplotypes with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	248
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	249 <data format="tabular" name="out_hapstats" label="Haplotype-based summary statistics for each locus in each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hapstats.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	250
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	251 <data format="tabular" name="out_populations_log" label="Populations log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.populations.log"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	252
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	253 <data format="tabular" name="out_sumstats_sum" label="Summary of summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats_summary.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	254
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	255 <data format="tabular" name="out_sumstats" label="Summary statistics for each population with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.sumstats.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	256
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	257 <data format="tabular" name="out_sql" label="Stacks SQL format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.markers.tsv"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	258
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	259 <data format="tabular" name="out_fstats" label="SNP and Haplotype-based F statistics with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phistats.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	260 <filter>fstats</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	261 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	262 <data format="tabular" name="out_fasta" label="Full sequence for each unique haplotype (regardless of plausibility) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fa">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	263 <filter>populations_output['fasta']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	264 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	265 <data format="tabular" name="out_phylip_all_partitions" label="Phylip all (partitions) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fullseq.partitions.phylip">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	266 <filter>populations_output['phylip_var_all']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	267 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	268 <data format="tabular" name="out_phylip_all_pop" label="Phylip all (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.fullseq.phylip">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	269 <filter>populations_output['phylip_var_all']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	270 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	271 <data format="tabular" name="out_phylip_all_loci" label="Phylip all (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1fullseq.phylip.log">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	272 <filter>populations_output['phylip_var_all']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	273 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	274 <data format="tabular" name="out_genepop" label="GenePop formatwith ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genepop">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	275 <filter>populations_output['genepop']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	276 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	277 <data format="tabular" name="out_vcf_haplotypes" label="Haplotypes in VCF format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.haplotypes.vcf">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	278 <filter>populations_output['vcf_haplotypes']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	279 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	280 <data format="tabular" name="out_hzar" label="Genotypes in Hybrid Zone Analysis using R (HAZR) format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.hzar.csv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	281 <filter>populations_output['hzar']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	282 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	283 <data format="tabular" name="out_beagle_phased_haplotypes" label="Beagle format (phased, haplotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.phased.bgl">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	284 <filter>populations_output['beagle_phased']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	285 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	286 <data format="tabular" name="out_beagle_phased_markers" label="Beagle format (phased, markers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.phased.bgl.markers">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	287 <filter>populations_output['beagle_phased']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	288 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	289 <data format="tabular" name="out_beagle_haplotypes" label="Beagle format (haplotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.unphased.bgl">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	290 <filter>populations_output['beagle']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	291 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	292 <data format="tabular" name="out_beagle_markers" label="Beagle format (markers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.myPopA-un.unphased.bgl.markers">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	293 <filter>populations_output['beagle']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	294 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	295 <data format="tabular" name="out_phylip_pop" label="Phylip (pop) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	296 <filter>populations_output['phylip']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	297 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	298 <data format="tabular" name="out_phylip_loci" label="Phylip (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.phylip.log">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	299 <filter>populations_output['phylip']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	300 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	301 <data format="tabular" name="out_plink_markers" label="PLINK (makers) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.plink.map">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	302 <filter>populations_output['plink']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	303 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	304 <data format="tabular" name="out_plink_genotypes" label="PLINK format (genotypes) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.plink.ped">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	305 <filter>populations_output['plink']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	306 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	307 <data format="tabular" name="out_fasta_strict" label="Full sequence for each haplotype (only for biologically plausible loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.strict.fa">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	308 <filter>populations_output['fasta_strict']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	309 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	310 <data format="tabular" name="out_structure" label="Structure format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.structure.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	311 <filter>populations_output['structure']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	312 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	313 <data format="tabular" name="out_treemix_pop" label="TreeMix format (population) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.treemix">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	314 <filter>populations_output['treemix']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	315 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	316 <data format="tabular" name="out_treemix_loci" label="TreeMix format (loci) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.treemix.log">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	317 <filter>populations_output['treemix']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	318 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	319 <data format="tabular" name="out_fastpĥase" label="fastPHASE format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.un.fastphase.inp">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	320 <filter>populations_output['fastphase']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	321 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	322 <data format="tabular" name="out_phase" label="PHASE format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.un.phase.inp">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	323 <filter>populations_output['phase']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	324 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	325 <data format="tabular" name="out_vcf" label="SNPs in VCF format with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.vcf">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	326 <filter>populations_output['vcf']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	327 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	328 <data format="tabular" name="out_genomic" label="Each nucleotide position in all population members with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.genomic.tsv">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	329 <filter>populations_output['options_genomic']['genomic']</filter>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	330 </data>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	331
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	332 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	333
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	334 <xml name="snp_options">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	335 <conditional name="select_model">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	336 <param name="model_type" type="select" label="Choose the model">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	337 <option value="snp" selected="true">SNP</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	338 <option value="bounded">Bounded SNP</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	339 <option value="fixed">Fixed</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	340 </param>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	341 <when value="snp">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	342 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	343 <option value="0.1">0.1</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	344 <option value="0.05" selected="True">0.05</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	345 <option value="0.01">0.01</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	346 <option value="0.001">0.001</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	347 </param>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	348 </when>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	349 <when value="bounded">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	350 <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	351 <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	352 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	353 <option value="0.1">0.1</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	354 <option value="0.05" selected="True">0.05</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	355 <option value="0.01">0.01</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	356 <option value="0.001">0.001</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	357 </param>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	358 </when>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	359 <when value="fixed">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	360 </when>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	361 </conditional>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	362 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	363
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	364 <xml name="snp_options_full">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	365 <conditional name="select_model">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	366 <param name="model_type" type="select" label="Choose the model">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	367 <option value="snp" selected="true">SNP</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	368 <option value="bounded">Bounded SNP</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	369 <option value="fixed">Fixed</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	370 </param>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	371 <when value="snp">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	372 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	373 <option value="0.1">0.1</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	374 <option value="0.05" selected="True">0.05</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	375 <option value="0.01">0.01</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	376 <option value="0.001">0.001</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	377 </param>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	378 </when>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	379 <when value="bounded">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	380 <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	381 <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	382 <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	383 <option value="0.1">0.1</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	384 <option value="0.05" selected="True">0.05</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	385 <option value="0.01">0.01</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	386 <option value="0.001">0.001</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	387 </param>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	388 </when>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	389 <when value="fixed">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	390 <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	391 </when>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	392 </conditional>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	393 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	394
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	395 <xml name="barcode_encoding_single">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	396 <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	397 <option value="--index_null">Barcode is provided in FASTQ header</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	398 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	399
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	400 <xml name="barcode_encoding_pair">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	401 <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	402 <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	403 <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	404 <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	405 <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	406 <option value="--inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	407 <option value="--index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	408 </xml>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: diff changeset	409 </macros>

Mercurial > repos > iuc > stacks_clonefilter

annotate macros.xml @ 0:a8a0cd05d47d draft