Mercurial > repos > matthias > stacks2_denovomap
annotate macros.xml @ 2:fa593b13402f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
| author | matthias |
|---|---|
| date | Tue, 18 Dec 2018 12:57:35 -0500 |
| parents | 58b5c841fa51 |
| children | 33ca88a71f08 |
| rev | line source |
|---|---|
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0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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1 <?xml version="1.0"?> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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2 <macros> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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3 <xml name="requirements"> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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4 <requirements> |
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1
58b5c841fa51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
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5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> |
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0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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6 <yield/> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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7 </requirements> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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8 </xml> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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9 |
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1
58b5c841fa51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
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10 <token name="@STACKS_VERSION@">2.2</token> |
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2
fa593b13402f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
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11 <token name="@WRAPPER_VERSION@">2</token> |
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0
e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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12 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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13 <xml name="stdio"> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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14 <stdio> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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15 <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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16 </stdio> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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17 </xml> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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18 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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19 <xml name="citation"> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
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20 <citations> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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21 <citation type="doi">10.1111/mec.12354</citation> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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22 <citation type="doi">10.1111/mec.12330</citation> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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23 <citation type="doi">10.1534/g3.111.000240</citation> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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24 <citation type="doi">10.1534/genetics.111.127324</citation> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
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25 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
diff
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26 <citation type="doi">10.1073/pnas.1006538107</citation> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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27 </citations> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
parents:
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28 </xml> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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29 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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30 <xml name="version_cmd"> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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31 <version_command><![CDATA[ |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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32 process_radtags -h |& grep process_radtags | head -n 1 | cut -d" " -f 2 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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33 ]]> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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34 </version_command> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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35 </xml> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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36 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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37 <token name="@STACKS_INFOS@"> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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38 <![CDATA[ |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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39 -------- |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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40 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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41 **Created by:** |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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42 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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43 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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44 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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45 **Project links:** |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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46 |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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47 `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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48 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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49 `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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50 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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51 `Stacks google group <http://groups.google.com/group/stacks-users>`_ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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52 ]]></token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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53 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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54 <xml name="enzymes"> |
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e5e5617c064a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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55 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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56 <option value="">Unspecified</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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57 <option value="aciI">aciI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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58 <option value="ageI">ageI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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59 <option value="aluI">aluI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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60 <option value="apaLI">apaLI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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61 <option value="apeKI">apeKI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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62 <option value="apoI">apoI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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63 <option value="aseI">aseI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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64 <option value="bamHI">bamHI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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65 <option value="bbvCI">bbvCI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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66 <option value="bfaI">bfaI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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67 <option value="bfuCI">bfuCI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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68 <option value="bgIII">bgIII</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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69 <option value="bsaHI">bsaHI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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70 <option value="bspDI">bspDI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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71 <option value="bstYI">bstYI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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72 <option value="cac8I">cac8I</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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73 <option value="claI">claI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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74 <option value="csp6I">csp6I</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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75 <option value="ddeI">ddeI</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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76 <option value="dpnII">dpnII</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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77 <option value="eaeI">eaeI</option> |
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78 <option value="ecoRI">ecoRI</option> |
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79 <option value="ecoRV">ecoRV</option> |
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80 <option value="ecoT22I">ecoT22I</option> |
|
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81 <option value="haeIII">haeIII</option> |
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82 <option value="hindIII">hindIII</option> |
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83 <option value="hinP1I">hinP1I</option> |
|
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84 <option value="hpaII">hpaII</option> |
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85 <option value="kpnI">kpnI</option> |
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86 <option value="mluCI">mluCI</option> |
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87 <option value="mseI">mseI</option> |
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88 <option value="mslI">mslI</option> |
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89 <option value="mspI">mspI</option> |
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90 <option value="ncoI">ncoI</option> |
|
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91 <option value="ndeI">ndeI</option> |
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92 <option value="nheI">nheI</option> |
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93 <option value="nlaIII">nlaIII</option> |
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94 <option value="notI">notI</option> |
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95 <option value="nsiI">nsiI</option> |
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96 <option value="nspI">nspI</option> |
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97 <option value="pstI">pstI</option> |
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98 <option value="rsaI">rsaI</option> |
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99 <option value="sacI">sacI</option> |
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100 <option value="sau3AI">sau3AI</option> |
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101 <option value="sbfI">sbfI</option> |
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102 <option value="sexAI">sexAI</option> |
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103 <option value="sgrAI">sgrAI</option> |
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104 <option value="speI">speI</option> |
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105 <option value="sphI">sphI</option> |
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106 <option value="taqI">taqI</option> |
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107 <option value="xbaI">xbaI</option> |
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108 <option value="xhoI">xhoI</option> |
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109 </xml> |
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110 |
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111 <!-- log file handling --> |
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112 <token name="@TEE_APPEND_LOG@"><![CDATA[ |
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113 #if $output_log |
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114 2>> $output_log && |
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115 #end if |
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116 ]]></token> |
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117 <token name="@CAT_LOG_TO_STDERR@"><![CDATA[ |
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118 #if $output_log |
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119 cat $output_log 2>&1 |
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120 #end if |
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121 ]]></token> |
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122 <xml name="in_log"> |
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123 <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as data set" /> |
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124 </xml> |
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125 <xml name="out_log"> |
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126 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> |
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127 <filter>add_log</filter> |
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128 </data> |
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129 </xml> |
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130 |
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131 |
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132 <!-- fastq input --> |
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133 <xml name="fastq_input_macro" token_fastq_optional="false"> |
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134 <conditional name="input_type"> |
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135 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"> |
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136 <option value="manual" selected="true">single end or forward reads</option> |
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137 <option value="list">(paired) data set list</option> |
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138 </param> |
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139 <when value="manual"> |
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140 <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> |
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141 </when> |
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142 <when value="list"> |
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143 <param name="samples" 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@"/> |
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0
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144 </when> |
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145 </conditional> |
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146 </xml> |
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147 <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set |
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148 appends noting/.1/.2 to the link name for accessing the fastq data |
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149 sets variables $name and $data_path--> |
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150 <token name="@FASTQ_INPUT@"><![CDATA[ |
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151 ## TODO should use sample.identidfier if possible (see corresp. preproc macro) |
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152 #set $name = $clean_ext($sample.name) |
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153 #set $data_path = "stacks_inputs/" + $name |
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154 #if $sample.is_collection: |
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155 #set $cur_sample=$sample[$read_direction] |
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156 #else: |
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157 #set $cur_sample=$sample |
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158 #end if |
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159 #if $read_direction == "forward": |
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160 #set $data_path = $data_path + ".1" |
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161 #elif $read_direction == "reverse": |
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162 #set $data_path = $data_path + ".2" |
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163 #end if |
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164 #if $cur_sample.is_of_type('fastqsanger') |
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165 #set $data_path = $data_path + ".fq" |
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166 #set inputype = "fastq" |
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167 #else if $cur_sample.is_of_type('fastqsanger.gz') |
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168 #set $data_path = $data_path + ".fq.gz" |
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169 #set inputype = "gzfastq" |
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170 #else if $cur_sample.is_of_type('fasta') |
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171 #set $data_path = $data_path + ".fa" |
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172 #set inputype = "fasta" |
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173 #else |
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174 #set $data_path = $data_path + ".fa.gz" |
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175 #set inputype = "gzfasta" |
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176 #end if |
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177 ln -s '$cur_sample' '${data_path}' && |
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178 ]]></token> |
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179 |
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180 <!-- macro and token for BAM input--> |
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181 <xml name="bam_input_macro"> |
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182 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" /> |
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183 </xml> |
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184 <token name="@BAM_INPUT@"><![CDATA[ |
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185 #set $bamlist = "" |
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186 #for $bam in $input_bam: |
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187 #set $filename = $clean_ext($bam.element_identifier)+".bam" |
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188 #if re.search('.*\.bam$', $filename) |
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189 ln -s '$bam' bam_inputs/$filename && |
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190 #set bamlist += " -B 'bam_inputs/"+$filename+"'" |
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191 #end if |
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192 #end for |
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193 ]]></token> |
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194 |
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195 <token name="@CLEAN_EXT@"> |
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196 <![CDATA[ |
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197 #from os.path import splitext |
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198 #import re |
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199 #def clean_ext($identifier) |
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200 #while $identifier.endswith(('.1', '.2', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) |
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201 #set $identifier = splitext($identifier)[0] |
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202 #end while |
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203 $identifier#slurp |
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204 #end def |
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205 ]]> |
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206 </token> |
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207 |
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208 <!-- tokens and macros for gapped alignment options |
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209 the _onoff macro gives an empty conditional (which is not so nice |
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210 but allows to be used also in the full macro) --> |
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211 <token name="@GAP_OPTIONS@"><![CDATA[ |
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212 #if $gapped.use_gapped == "yes" |
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213 --max_gaps $gapped.max_gaps |
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214 --min_aln_len $gapped.min_aln_len |
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215 #else |
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216 --disable-gapped |
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217 #end if |
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218 ]]></token> |
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219 <token name="@GAP_OPTIONS_ONOFF@"><![CDATA[ |
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220 #if $gapped.use_gapped != "yes" |
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221 --disable-gapped |
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222 #end if |
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223 ]]></token> |
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224 <xml name="gap_options"> |
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225 <expand macro="gap_options_onoff"> |
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226 <param argument="--max_gaps" type="float" value="2.0" label="Number of gaps allowed between stacks before merging"/> |
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227 <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"/> |
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228 </expand> |
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229 </xml> |
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230 <xml name="gap_options_onoff"> |
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231 <conditional name="gapped"> |
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232 <param name="use_gapped" argument="--disable-gapped" type="select" label="Perform gapped alignments between stacks"> |
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233 <option value="no">No</option> |
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234 <option value="yes" selected="true">Yes</option> |
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235 </param> |
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236 <when value="no"/> |
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237 <when value="yes"> |
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238 <yield/> |
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239 </when> |
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240 </conditional> |
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241 </xml> |
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242 |
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243 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> |
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244 <!-- TODO tags, snps, and alleles could go to sub collections --> |
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245 <xml name="ustacks_outputs_macro" token_tooladd=""> |
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246 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks"> |
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247 <discover_datasets pattern="(?P<name>(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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248 <discover_datasets pattern="(?P<name>(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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249 <discover_datasets pattern="(?P<name>(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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250 </collection> |
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251 </xml> |
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252 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv --> |
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253 <xml name="cstacks_outputs_macro" token_tooladd=""> |
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254 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog"> |
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255 <discover_datasets pattern="(?P<name>catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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256 </collection> |
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257 </xml> |
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258 <!-- sstacks outputs collection containing SAMPLE.matches.tsv --> |
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259 <xml name="sstacks_outputs_macro" token_tooladd=""> |
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260 <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog"> |
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261 <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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262 </collection> |
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263 </xml> |
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264 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam --> |
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265 <xml name="tsv2bam_outputs_macro" token_tooladd=""> |
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266 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks"> |
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267 <discover_datasets pattern="(?P<name>.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" /> |
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268 </collection> |
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269 </xml> |
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270 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz --> |
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271 <xml name="gstacks_outputs_macro" token_tooladd=""> |
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272 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string}"> |
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273 <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" /> |
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274 <discover_datasets pattern="(?P<name>catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" /> |
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275 </collection> |
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276 </xml> |
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277 |
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278 <!-- default output of populations --> |
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279 <xml name="populations_output_light" token_tooladd=""> |
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280 <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" /> |
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281 <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" /> |
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282 <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" /> |
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283 <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" /> |
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284 <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" /> |
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285 <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" /> |
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286 </xml> |
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287 |
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288 <xml name="populations_output_full"> |
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289 <expand macro="populations_output_light"/> |
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290 |
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291 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> |
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292 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> |
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293 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> |
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294 </data> |
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295 <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv"> |
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296 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> |
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297 </data> |
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298 <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv"> |
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299 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> |
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300 </data> |
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301 |
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302 <!-- fasta_loci populations.loci.fa |
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303 fasta_samples populations.samples.fa |
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304 fasta_samples_raw populations.samples-raw.fa--> |
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305 <data format="tabular" name="out_fasta_strict" label="${tool.name} on ${on_string} per-locus consensus sequences" from_work_dir="stacks_outputs/populations.loci.fa"> |
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306 <filter>populations_output['fasta_loci']</filter> |
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307 </data> |
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308 <data format="tabular" name="out_fasta" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences" from_work_dir="stacks_outputs/populations.samples.fa"> |
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309 <filter>populations_output['fasta_samples']</filter> |
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310 </data> |
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311 <data format="tabular" name="out_fasta_raw" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences (regardless of biological plausibility)" from_work_dir="stacks_outputs/populations.samples-raw.fa"> |
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312 <filter>populations_output['fasta_samples_raw']</filter> |
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313 </data> |
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314 |
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315 <!-- phylip populations.fixed.phylip populations.fixed.phylip.log |
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316 phylip_var populations.var.phylip populations.var.phylip.log--> |
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317 <data format="tabular" name="out_phylip_all_pop_fix" label="${tool.name} on ${on_string} Phylip nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip"> |
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318 <filter>populations_output['phylip']</filter> |
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319 </data> |
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320 <data format="tabular" name="out_phylip_all_loci_fix" label="${tool.name} on ${on_string} Phylip (loci) nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip.log"> |
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321 <filter>populations_output['phylip']</filter> |
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322 </data> |
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323 <data format="tabular" name="out_phylip_all_pop_var" label="${tool.name} on ${on_string} Phylip all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip"> |
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324 <filter>populations_output['phylip_var']</filter> |
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325 </data> |
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326 <data format="tabular" name="out_phylip_all_loci_var" label="${tool.name} on ${on_string} Phylip (loci) all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip.log"> |
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327 <filter>populations_output['phylip_var']</filter> |
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328 </data> |
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329 |
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330 <!-- genepop populations.haps.genepop populations.snps.genepop --> |
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331 <data format="tabular" name="out_genepop_snps" label="${tool.name} on ${on_string} SNPs in GenePop format" from_work_dir="stacks_outputs/populations.snps.genepop"> |
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332 <filter>populations_output['genepop']</filter> |
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333 </data> |
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334 <data format="tabular" name="out_genepop_haps" label="${tool.name} on ${on_string} Haplotypes in GenePop format" from_work_dir="stacks_outputs/populations.haps.genepop"> |
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335 <filter>populations_output['genepop']</filter> |
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336 </data> |
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337 |
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338 <!-- vcf populations.haps.vcf populations.snps.vcf --> |
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339 <data format="vcf" name="out_vcf_haplotypes_snps" label="${tool.name} on ${on_string} SNPs in VCF format" from_work_dir="stacks_outputs/populations.snps.vcf"> |
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340 <filter>populations_output['vcf']</filter> |
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341 </data> |
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342 <data format="vcf" name="out_vcf_haplotypes_haps" label="${tool.name} on ${on_string} Haplotypes in VCF format" from_work_dir="stacks_outputs/populations.haps.vcf"> |
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343 <filter>populations_output['vcf']</filter> |
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344 </data> |
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345 |
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346 <!--plink populations.plink.map populations.plink.ped--> |
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347 <data format="tabular" name="out_plink_markers" label="${tool.name} on ${on_string} PLINK (makers)" from_work_dir="stacks_outputs/populations.plink.map"> |
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348 <filter>populations_output['plink']</filter> |
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349 </data> |
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350 <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped"> |
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351 <filter>populations_output['plink']</filter> |
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352 </data> |
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353 |
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354 <!--structure populations.structure--> |
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355 <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure"> |
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356 <filter>populations_output['structure']</filter> |
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357 </data> |
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358 |
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359 <!-- radpainter populations.haps.radpainter --> |
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360 <data format="tabular" name="out_radpainter" label="${tool.name} on ${on_string} Radpainter format" from_work_dir="stacks_outputs/populations.haps.radpainter"> |
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361 <filter>populations_output['radpainter']</filter> |
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362 </data> |
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363 |
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364 </xml> |
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365 |
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366 <xml name="snp_options_alpha"> |
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367 <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > |
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368 <option value="0.1">0.1</option> |
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369 <option value="0.05" selected="True">0.05</option> |
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370 <option value="0.01">0.01</option> |
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371 <option value="0.001">0.001</option> |
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372 </param> |
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373 </xml> |
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374 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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375 <xml name="snp_options"> |
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376 <conditional name="select_model"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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377 <param argument="--model_type" type="select" label="Choose the model"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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378 <option value="snp" selected="true">SNP</option> |
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379 <option value="bounded">Bounded SNP</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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380 <option value="fixed">Fixed</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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381 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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382 <when value="snp"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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383 <expand macro="snp_options_alpha"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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384 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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385 <when value="bounded"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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386 <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"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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387 <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" /> |
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388 <expand macro="snp_options_alpha"/> |
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389 </when> |
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390 <when value="fixed"> |
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391 <yield/> |
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392 </when> |
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393 </conditional> |
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394 </xml> |
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395 <xml name="snp_options_full"> |
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396 <expand macro="snp_options"> |
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397 <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"/> |
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398 </expand> |
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399 </xml> |
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400 |
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401 <!-- variant calling option for use in gstacks and denovomap --> |
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402 <xml name="variant_calling_options_vg"> |
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403 <param argument="--var-alpha" name="var_alpha" type="float" value="0.05" min="0" label="alpha threshold for discovering SNPs" /> |
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404 <expand macro="variant_calling_options_g"/> |
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405 </xml> |
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406 <xml name="variant_calling_options_g"> |
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407 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="alpha threshold for calling genotypes" /> |
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408 </xml> |
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409 |
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2
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410 <xml name="barcode_encoding_single" token_type=""> |
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411 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option> |
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412 <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option> |
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0
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413 <yield/> |
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414 </xml> |
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415 |
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2
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416 <xml name="barcode_encoding_pair" token_type=""> |
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417 <expand macro="barcode_encoding_single" type="@TYPE@"> |
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418 <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option> |
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419 <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option> |
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420 <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option> |
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421 <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> |
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422 <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> |
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0
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423 </expand> |
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424 </xml> |
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425 </macros> |