stacks2_clonefilter: macros.xml annotate

annotate macros.xml @ 1:b75174403a65 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"

author	iuc
date	Mon, 30 Sep 2019 14:19:47 -0400
parents	1b6d07160736
children	2f1d464ebfd2

rev	line source
0 1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	1 <?xml version="1.0"?>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	2 <macros>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	3 <xml name="requirements">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	4 <requirements>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	6 <yield/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	7 </requirements>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	8 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	9
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	10 <token name="@STACKS_VERSION@">2.4</token>
1 b75174403a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4" iuc parents: 0 diff changeset	11 <token name="@WRAPPER_VERSION@">1</token>
0 1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	12 <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	13 <token name="@PROFILE@">18.01</token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	14
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	15 <xml name="citation">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	16 <citations>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	17 <citation type="doi">10.1111/mec.12354</citation>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	18 <citation type="doi">10.1111/mec.12330</citation>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	19 <citation type="doi">10.1534/g3.111.000240</citation>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	20 <citation type="doi">10.1534/genetics.111.127324</citation>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	21 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	22 <citation type="doi">10.1073/pnas.1006538107</citation>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	23 </citations>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	24 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	25
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	26 <xml name="version_cmd">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	27 <version_command><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	28 process_radtags -h \|& grep process_radtags \| head -n 1 \| cut -d" " -f 2
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	29 ]]>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	30 </version_command>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	31 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	32
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	33 <token name="@STACKS_INFOS@">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	34 <![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	35 --------
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	36
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	37 Created by:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	38
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	39 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	40
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	41 Project links:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	42
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	43 `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	44
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	45 `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	46
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	47 `Stacks google group <http://groups.google.com/group/stacks-users>`_
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	48 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	49
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	50 <!-- enzyme list for procrad and denovo -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	51 <xml name="enzymes">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	52 <option value="">Unspecified</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	53 <option value="aciI">aciI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	54 <option value="ageI">ageI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	55 <option value="aluI">aluI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	56 <option value="apaLI">apaLI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	57 <option value="apeKI">apeKI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	58 <option value="apoI">apoI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	59 <option value="aseI">aseI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	60 <option value="bamHI">bamHI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	61 <option value="bbvCI">bbvCI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	62 <option value="bfaI">bfaI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	63 <option value="bfuCI">bfuCI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	64 <option value="bgIII">bgIII</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	65 <option value="bsaHI">bsaHI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	66 <option value="bspDI">bspDI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	67 <option value="bstYI">bstYI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	68 <option value="cac8I">cac8I</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	69 <option value="claI">claI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	70 <option value="csp6I">csp6I</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	71 <option value="ddeI">ddeI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	72 <option value="dpnII">dpnII</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	73 <option value="eaeI">eaeI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	74 <option value="ecoRI">ecoRI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	75 <option value="ecoRV">ecoRV</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	76 <option value="ecoT22I">ecoT22I</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	77 <option value="haeIII">haeIII</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	78 <option value="hindIII">hindIII</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	79 <option value="hinP1I">hinP1I</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	80 <option value="hpaII">hpaII</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	81 <option value="kpnI">kpnI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	82 <option value="mluCI">mluCI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	83 <option value="mseI">mseI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	84 <option value="mslI">mslI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	85 <option value="mspI">mspI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	86 <option value="ncoI">ncoI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	87 <option value="ndeI">ndeI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	88 <option value="nheI">nheI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	89 <option value="nlaIII">nlaIII</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	90 <option value="notI">notI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	91 <option value="nsiI">nsiI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	92 <option value="nspI">nspI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	93 <option value="pstI">pstI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	94 <option value="rsaI">rsaI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	95 <option value="sacI">sacI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	96 <option value="sau3AI">sau3AI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	97 <option value="sbfI">sbfI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	98 <option value="sexAI">sexAI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	99 <option value="sgrAI">sgrAI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	100 <option value="speI">speI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	101 <option value="sphI">sphI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	102 <option value="taqI">taqI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	103 <option value="xbaI">xbaI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	104 <option value="xhoI">xhoI</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	105 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	106
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	107 <!-- log file handling -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	108 <token name="@TEE_APPEND_LOG@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	109 #if $output_log
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	110 2>> '$output_log' &&
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	111 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	112 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	113 <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	114 #if $output_log
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	115 cat '$output_log' 2>&1
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	116 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	117 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	118 <xml name="in_log">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	119 <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	120 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	121 <xml name="out_log">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	122 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	123 <filter>add_log</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	124 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	125 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	126
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	127 <!-- inputs from previous pipeline steps -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	128 <xml name="input_stacks_macro">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	129 <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	130 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	131 <xml name="input_cat_macro">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	132 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	133 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	134 <xml name="input_matches_macro">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	135 <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	136 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	137 <xml name="bam_input_macro">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	138 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	139 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	140 <xml name="input_aln_macro">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	141 <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	142 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	143
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	144 <!-- code for creating links to the data sets from previous pipeline steps
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	145 - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	146 also stores sample names in list (samples)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	147 - cat (cstacks catalog.tags.tsv, catalog.alleles.tsv, catalog.snps.tsv)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	148 - matches (sstacks POP.matches.tsv) -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	149 <token name="@LINK_STACKS_INPUT@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	150 #set $samples = []
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	151 #for $input_file in $input_stacks
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	152 #set $filename = str($input_file.element_identifier)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	153 #if not filename.endswith('.tsv')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	154 #set $filename = $filename + ".tsv"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	155 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	156 #if re.search('^(?!catalog).+\.(tags\|alleles\|snps)\.tsv$', $filename)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	157 ln -s '${input_file}' 'stacks_inputs/$filename' &&
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	158 #if $filename.endswith('.tags.tsv')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	159 $samples.append($filename[:-9])
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	160 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	161 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	162 #end for
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	163 ]]>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	164 </token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	165 <token name="@LINK_CAT_INPUT@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	166 #for $input_file in $input_cat
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	167 #set $filename = str($input_file.element_identifier)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	168 #if not filename.endswith('.tsv')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	169 #set $filename = $filename + ".tsv"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	170 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	171 #if re.search('^catalog\.(tags\|alleles\|snps)\.tsv$', $filename)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	172 ln -s '${input_file}' 'stacks_inputs/$filename' &&
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	173 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	174 #end for
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	175 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	176 <token name="@LINK_MATCHES_INPUT@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	177 #for $input_file in $input_matches
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	178 #set $filename = str($input_file.element_identifier)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	179 #if not filename.endswith('.tsv')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	180 #set $filename = $filename + ".tsv"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	181 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	182 #if re.search('matches.tsv$', $filename)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	183 ln -s '${input_file}' 'stacks_inputs/$filename' &&
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	184 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	185 #end for
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	186 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	187
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	188 <!-- fastq input for process_radtags/shortreads (non-batch) and clone/kmerfilter (batch)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	189 for batch processing chose multiple=false and paired
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	190 otherwise multiple=true and listtype=list:paired -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	191 <xml name="fastq_input_bc" token_multiple="false" token_listtype="paired">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	192 <conditional name="input_type">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	193 <param name="input_type_select" type="select" label="Single-end or paired-end reads">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	194 <option value="single" selected="True">Single-end files</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	195 <option value="paired">Paired-end files</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	196 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	197 <when value="single">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	198 <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	199 <param name="barcode_encoding" type="select" label="Barcode location">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	200 <expand macro="barcode_encoding_single" type="Barcode" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	201 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	202 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	203 <when value="paired">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	204 <param name="fqinputs" type="data_collection" collection_type="@LISTTYPE@" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	205 <param name="barcode_encoding" type="select" label="Barcode location">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	206 <expand macro="barcode_encoding_pair" type="Barcode" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	207 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	208 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	209 </conditional>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	210 <yield/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	211 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	212
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	213 <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	214 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	215 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	216 </expand>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	217 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	218
1 b75174403a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4" iuc parents: 0 diff changeset	219 <!-- fastq input (used in denovomap, tsv2bam, ustacks)
b75174403a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4" iuc parents: 0 diff changeset	220 - fastq_optional: makes fastq input optional (true/false)
0 1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	221 - se_option: wording for "single end" option (for tsv2bam this is the
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	222 reverse reads for the others its the forward reads)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	223 - help: help text -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	224 <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	225 <conditional name="input_type">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	226 <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	227 <option value="single" selected="true">@SE_OPTION@</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	228 <option value="paired">(paired) dataset list</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	229 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	230 <when value="single">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	231 <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	232 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	233 <when value="paired">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	234 <param name="fqinputs" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	235 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	236 </conditional>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	237 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	238
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	239 <!-- helper functions for linking fastq data sets -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	240 <token name="@FASTQ_INPUT_FUNCTIONS@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	241 #from os.path import splitext
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	242 #import re
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	243
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	244 #def clean_ext($identifier)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	245 #while $identifier.endswith(('.1', '.2', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	246 #set $identifier = splitext($identifier)[0]
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	247 #end while
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	248 $identifier#slurp
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	249 #end def
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	250
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	251 #def fastq_input_foo( $sample, $read_direction="", $infix="" )
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	252 #set $name = $clean_ext($sample.element_identifier)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	253 #if $sample.is_collection:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	254 #set $cur_sample=$sample[$read_direction]
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	255 #else:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	256 #set $cur_sample=$sample
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	257 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	258
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	259 #if $cur_sample.is_of_type('fastqsanger')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	260 #set $ext = "fastq"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	261 #set $inputype = "fastq"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	262 #else if $cur_sample.is_of_type('fastqsanger.gz')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	263 #set $ext = "fastq.gz"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	264 #set $inputype = "gzfastq"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	265 #else if $cur_sample.is_of_type('fasta')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	266 #set $ext = "fasta"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	267 #set $inputype = "fasta"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	268 #else if $cur_sample.is_of_type('fasta.gz')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	269 #set $ext = "fasta.gz"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	270 #set $inputype = "gzfasta"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	271 #else
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	272 #set $inputype = "UNKNOWN"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	273 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	274 #set $data_path = "stacks_inputs/"+$name+$infix+"."+$ext
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	275 #set $link_cmd = "ln -s '%s' '%s' &&" % ($cur_sample, $data_path)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	276 #return ($link_cmd, $data_path, $name, $inputype)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	277 #end def
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	278
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	279 ## fastq_input_batch determine link command, access path(s), and input type
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	280 ## for batch tools
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	281 ##
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	282 ## inputs
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	283 ## - sample data set / pair
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	284 ## - type "single" / "paired"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	285 ## return (link_command, fwd_path, rev_path, inputype)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	286 ## - link_command bash command(s) to link the data sets
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	287 ## - fwd_path file name of the link to the forward data set
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	288 ## - rev_path file name of the link to the forward data set (if type=paired)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	289 ## - inputype input type as used in stacks ([gz]fast(a\|q))
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	290 #def fastq_input_batch($sample, $type)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	291 #if $type == "single"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	292 #set ($link_cmd, $path, $name, $inputype) = $fastq_input_foo($sample, "", "")
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	293 #return ($link_cmd, $path, "", $inputype)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	294 #else:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	295 #set ($fwd_link_cmd, $fwd_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	296 #set ($rev_link_cmd, $rev_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2")
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	297 #return ( $fwd_link_cmd+$rev_link_cmd, $fwd_path, $rev_path, $inputype)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	298 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	299 #end def
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	300
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	301 ## fastq_input_nonbatch determine link command, access path(s), and input type
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	302 ## for non-batch tools (procrad, shortreads, denovomap the former need R[12]_
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	303 ## and the latter needs .[12])
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	304 ##
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	305 ## inputs
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	306 ## - samples list of data set / pair
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	307 ## - type "single" / "paired"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	308 ## - infix_pattern pattern for the infix of the files (needs to contain %d which is replaced by 1/2)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	309 ## return (link_command, inputype)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	310 ## - link_command bash command(s) to link the data sets
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	311 ## - inputype input type as used in stacks ([gz]fast(a\|q))
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	312 #def fastq_input_nonbatch( $samples, $type, $infix_pattern )
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	313 #set $link_command = ""
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	314 #for $sample in $samples
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	315 #if $type == "single"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	316 #set ($lc, $path, $name, $inputype) = $fastq_input_foo($sample, "", "")
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	317 #set link_command += lc
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	318 #else:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	319 #set ($lc, $path, $name, $inputype) = $fastq_input_foo($sample, "forward", $infix_pattern % (1))
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	320 #set link_command += lc
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	321 #set ($lc, $path, $name, $inputype) = $fastq_input_foo($sample, "reverse", $infix_pattern % (2))
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	322 #set link_command += lc
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	323 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	324 #end for
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	325 #return ($link_command, $inputype)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	326 #end def
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	327 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	328
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	329 <!-- macro and token for BAM input, for each bam file w identifier NAME
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	330 - creates a link NAME.bam <- bam_inputs/NAME.INFIX.bam
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	331 - appends -B bam_inputs/NAME.INFIX.bam to variable bamlist
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	332
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	333 INFIX is set to"" per default, can be set with optional variable $infix
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	334 only needed for gstacks in denovo mode which needs .matches.bam -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	335 <token name="@BAM_INPUT@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	336 #set $bamlist = ""
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	337 #for $bam in $input_bam:
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	338 #if $bam.is_of_type('bam')
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	339 #set $filename = $clean_ext($bam.element_identifier)+".bam"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	340 ln -s '$bam' bam_inputs/$filename &&
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	341 #set bamlist += " -B 'bam_inputs/"+$filename+"'"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	342 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	343 #end for
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	344 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	345
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	346 <token name="@EXTRACT_VCF@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	347 ## the catalog.calls output is a gzip-ed vcf extract it
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	348 ## to make it usable in Galaxy (with the downside that we
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	349 ## need to gzip it again for downstream calls like populations)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	350 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	351 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	352
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	353
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	354
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	355 <!-- tokens and macros for gapped alignment options
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	356 the _onoff macro gives an empty conditional (which is not so nice
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	357 but allows to be used also in the full macro) -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	358 <token name="@GAP_OPTIONS@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	359 #if $gapped.use_gapped == "yes"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	360 --max_gaps $gapped.max_gaps
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	361 --min_aln_len $gapped.min_aln_len
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	362 #else
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	363 --disable-gapped
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	364 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	365 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	366 <token name="@GAP_OPTIONS_ONOFF@"><![CDATA[
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	367 #if $gapped.use_gapped != "yes"
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	368 --disable-gapped
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	369 #end if
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	370 ]]></token>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	371 <xml name="gap_options">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	372 <expand macro="gap_options_onoff">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	373 <param argument="--max_gaps" type="float" value="2.0" label="Number of gaps allowed between stacks before merging"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	374 <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	375 </expand>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	376 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	377 <xml name="gap_options_onoff">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	378 <conditional name="gapped">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	379 <param name="use_gapped" argument="--disable-gapped" type="select" label="Perform gapped alignments between stacks">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	380 <option value="no">No</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	381 <option value="yes" selected="true">Yes</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	382 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	383 <when value="no"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	384 <when value="yes">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	385 <yield/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	386 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	387 </conditional>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	388 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	389
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	390
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	391 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	392 <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	393 <xml name="ustacks_outputs_macro" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	394 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci and polymorphism">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	395 <discover_datasets pattern="(?P<name>(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	396 <discover_datasets pattern="(?P<name>(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	397 <discover_datasets pattern="(?P<name>(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	398 </collection>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	399 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	400 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	401 <xml name="cstacks_outputs_macro" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	402 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	403 <discover_datasets pattern="(?P<name>catalog\.(tags\|snps\|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	404 </collection>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	405 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	406 <!-- sstacks outputs collection containing SAMPLE.matches.tsv -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	407 <xml name="sstacks_outputs_macro" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	408 <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	409 <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	410 </collection>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	411 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	412 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	413 <xml name="tsv2bam_outputs_macro" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	414 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog (bam)">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	415 <discover_datasets pattern="(?P<name>.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	416 </collection>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	417 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	418 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	419 + optional output alignments.bam (if no popmap is given) and POP.alns.bam otherwise-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	420 <xml name="gstacks_outputs_full_macro" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	421 <expand macro="gstacks_outputs_macro"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	422 <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	423 <filter>add_log_distribs</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	424 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	425 <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	426 <discover_datasets pattern="(?P<name>.*).alns.bam$" ext="bam" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	427 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	428 </collection>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	429 <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	430 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	431 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	432 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	433 <xml name="gstacks_outputs_macro" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	434 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	435 <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	436 <discover_datasets pattern="(?P<name>catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	437 </collection>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	438 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	439
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	440 <!-- default output of populations -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	441 <xml name="populations_output_light" token_tooladd="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	442 <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	443 <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	444 <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	445 <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	446 <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	447 <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	448 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	449
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	450 <xml name="populations_output_full">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	451 <expand macro="populations_output_light"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	452
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	453 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	454 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	455 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	456 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	457 <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	458 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	459 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	460 <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	461 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	462 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	463
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	464 <!-- fasta_loci populations.loci.fa
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	465 fasta_samples populations.samples.fa
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	466 fasta_samples_raw populations.samples-raw.fa-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	467 <data format="tabular" name="out_fasta_strict" label="${tool.name} on ${on_string} per-locus consensus sequences" from_work_dir="stacks_outputs/populations.loci.fa">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	468 <filter>populations_output['fasta_loci']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	469 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	470 <data format="tabular" name="out_fasta" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences" from_work_dir="stacks_outputs/populations.samples.fa">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	471 <filter>populations_output['fasta_samples']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	472 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	473 <data format="tabular" name="out_fasta_raw" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences (regardless of biological plausibility)" from_work_dir="stacks_outputs/populations.samples-raw.fa">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	474 <filter>populations_output['fasta_samples_raw']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	475 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	476
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	477 <!-- phylip populations.fixed.phylip populations.fixed.phylip.log
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	478 phylip_var populations.var.phylip populations.var.phylip.log-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	479 <data format="tabular" name="out_phylip_all_pop_fix" label="${tool.name} on ${on_string} Phylip nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	480 <filter>populations_output['phylip']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	481 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	482 <data format="tabular" name="out_phylip_all_loci_fix" label="${tool.name} on ${on_string} Phylip (loci) nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip.log">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	483 <filter>populations_output['phylip']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	484 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	485 <data format="tabular" name="out_phylip_all_pop_var" label="${tool.name} on ${on_string} Phylip all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	486 <filter>populations_output['phylip_var']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	487 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	488 <data format="tabular" name="out_phylip_all_loci_var" label="${tool.name} on ${on_string} Phylip (loci) all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip.log">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	489 <filter>populations_output['phylip_var']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	490 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	491
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	492 <!-- genepop populations.haps.genepop populations.snps.genepop -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	493 <data format="tabular" name="out_genepop_snps" label="${tool.name} on ${on_string} SNPs in GenePop format" from_work_dir="stacks_outputs/populations.snps.genepop">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	494 <filter>populations_output['genepop']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	495 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	496 <data format="tabular" name="out_genepop_haps" label="${tool.name} on ${on_string} Haplotypes in GenePop format" from_work_dir="stacks_outputs/populations.haps.genepop">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	497 <filter>populations_output['genepop']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	498 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	499
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	500 <!-- vcf populations.haps.vcf populations.snps.vcf -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	501 <data format="vcf" name="out_vcf_haplotypes_snps" label="${tool.name} on ${on_string} SNPs in VCF format" from_work_dir="stacks_outputs/populations.snps.vcf">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	502 <filter>populations_output['vcf']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	503 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	504 <data format="vcf" name="out_vcf_haplotypes_haps" label="${tool.name} on ${on_string} Haplotypes in VCF format" from_work_dir="stacks_outputs/populations.haps.vcf">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	505 <filter>populations_output['vcf']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	506 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	507
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	508 <!--plink populations.plink.map populations.plink.ped-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	509 <data format="tabular" name="out_plink_markers" label="${tool.name} on ${on_string} PLINK (makers)" from_work_dir="stacks_outputs/populations.plink.map">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	510 <filter>populations_output['plink']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	511 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	512 <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	513 <filter>populations_output['plink']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	514 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	515
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	516 <!--structure populations.hzar-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	517 <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	518 <filter>populations_output['hzar']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	519 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	520 <!--structure populations.structure-->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	521 <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	522 <filter>populations_output['structure']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	523 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	524
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	525 <!-- radpainter populations.haps.radpainter -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	526 <data format="tabular" name="out_radpainter" label="${tool.name} on ${on_string} Radpainter format" from_work_dir="stacks_outputs/populations.haps.radpainter">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	527 <filter>populations_output['radpainter']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	528 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	529
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	530 <!-- treemix populations.treemix -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	531 <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	532 <filter>populations_output['treemix']</filter>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	533 </data>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	534 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	535
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	536 <xml name="snp_options_alpha">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	537 <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	538 <option value="0.1">0.1</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	539 <option value="0.05" selected="True">0.05</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	540 <option value="0.01">0.01</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	541 <option value="0.001">0.001</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	542 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	543 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	544
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	545 <xml name="snp_options">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	546 <conditional name="select_model">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	547 <param argument="--model_type" type="select" label="Choose the model">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	548 <option value="snp" selected="true">SNP</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	549 <option value="bounded">Bounded SNP</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	550 <option value="fixed">Fixed</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	551 </param>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	552 <when value="snp">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	553 <expand macro="snp_options_alpha"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	554 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	555 <when value="bounded">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	556 <param 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"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	557 <param 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" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	558 <expand macro="snp_options_alpha"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	559 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	560 <when value="fixed">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	561 <yield/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	562 </when>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	563 </conditional>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	564 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	565 <xml name="snp_options_full">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	566 <expand macro="snp_options">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	567 <param 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"/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	568 </expand>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	569 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	570
1 b75174403a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4" iuc parents: 0 diff changeset	571 <!-- variant calling option for use in gstacks and denovomap
0 1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	572 default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	573 otherwise no default is is available and gstacks will output and error
1 b75174403a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4" iuc parents: 0 diff changeset	574 "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
0 1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	575 -->
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	576 <xml name="variant_calling_options_vg" token_varalpha_default="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	577 <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	578 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	579 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	580
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	581 <xml name="barcode_encoding_single" token_type="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	582 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	583 <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	584 <yield/>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	585 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	586
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	587 <xml name="barcode_encoding_pair" token_type="">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	588 <expand macro="barcode_encoding_single" type="@TYPE@">
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	589 <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	590 <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	591 <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	592 <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	593 <option value="--index_inline">@TYPE@ 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) (--index_inline)</option>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	594 </expand>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	595 </xml>
1b6d07160736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 iuc parents: diff changeset	596 </macros>

Mercurial > repos > iuc > stacks2_clonefilter

annotate macros.xml @ 1:b75174403a65 draft