Mercurial > repos > iuc > obi_annotate
annotate obiannotate.xml @ 3:f82cefbbcea5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author | iuc |
---|---|
date | Mon, 10 May 2021 19:37:25 +0000 |
parents | 3d21aa00d575 |
children | d50dc96e3ce9 |
rev | line source |
---|---|
3
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
|
1 <tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@" profile="@PROFILE@"> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
|
2 <description>Adds/Edits sequence record annotations</description> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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3 <macros> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
|
4 <import>macros.xml</import> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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5 </macros> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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6 <expand macro="requirements"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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7 <expand macro="stdio"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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8 <command><![CDATA[ |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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9 @GUNZIP_INPUT@ |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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10 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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11 obiannotate |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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12 --without-progress-bar |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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13 ${seqrank} |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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14 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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15 #if $rename_tag.old_name and $rename_tag.new_name |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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16 -R '$rename_tag.old_name':'$rename_tag.new_name' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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17 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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18 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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19 #if $deletetag_key |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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20 --delete-tag='$deletetag_key' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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21 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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|
22 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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23 #if $set_tag.key and $set_tag.pythonexpression |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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24 -S '$set_tag.key':'$set_tag.pythonexpression' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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25 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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26 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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27 #if $taglist |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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28 --tag-list='$taglist' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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29 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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30 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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31 #if $setid_pythonexpression |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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32 --set-identifier='$setid_pythonexpression' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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33 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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34 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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35 #if $pythonexpression |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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36 --run='$pythonexpression' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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37 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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38 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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39 #if $setsequence_pythonexpression |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
diff
changeset
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40 --set-sequence='$setsequence_pythonexpression' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
diff
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41 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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42 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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changeset
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43 #if $setdefinition_pythonexpression |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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44 --set-definition='$setdefinition_pythonexpression' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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45 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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46 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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47 #if $key_selector.key |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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48 --keep='$key_selector.key' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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49 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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50 #if $key_selector.key2 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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51 --keep='$key_selector.key2' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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52 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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53 #if $key_selector.key3 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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54 --keep='$key_selector.key3' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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55 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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56 #if $key_selector.key4 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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57 --keep='$key_selector.key4' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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58 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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59 #if $key_selector.key5 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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60 --keep='$key_selector.key5' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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61 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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62 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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63 ${length} |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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64 ${clearbool} |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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65 ${uniqid} |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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66 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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67 #if $rankname |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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68 --with-taxon-at-rank='$rankname' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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69 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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70 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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71 #if $mclfile |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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72 --mcl='$mclfile' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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73 #end if |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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74 @INPUT_FORMAT@ |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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75 @OUT_FORMAT@ |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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76 input |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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77 @GZIP_OUTPUT@ |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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78 > '$output' |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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79 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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80 @GENERATE_GALAXY_JSON@ |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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81 ]]></command> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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82 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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83 <inputs> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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84 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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85 <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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86 <section name="rename_tag" title="Rename attribute" expanded="False"> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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87 <param name="old_name" type="text" label="old name" optional="true"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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88 <param name="new_name" type="text" label="new name" optional="true"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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89 </section> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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90 <param name="deletetag_key" type="text" label="Delete attribute" optional="true" help="Use this option if you want to delete attribute named ATTRIBUTE_NAME.When this attribute is missing, the sequence record is skipped and the next one is examined"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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91 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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92 <section name="set_tag" title="Create a new attribute" expanded="False"> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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93 <param name="key" type="text" label="key" optional="true"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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94 <param name="pythonexpression" type="text" label="python expression" optional="true"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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|
95 </section> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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96 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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97 <param name="taglist" type="data" optional="true" format="txt,tabular" label="Use a tag list" help="file containing identifiers of sequences to select" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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98 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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99 <param name="setid_pythonexpression" type="text" label="Set sequence record identifier with a value" help="Use this option if you want to set sequence record identifier with a value computed from PYTHON_EXPRESSION" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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100 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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101 <param name="pythonexpression" type="text" label="Run a PYTHON_EXPRESSION on each selected sequence" optional="true" help="Use this option if you want to run a PYTHON_EXPRESSION on each selected sequence"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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102 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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103 <param name="setsequence_pythonexpression" type="text" label="Change the sequence itself with a value" help="Use this option if you want to change the sequence itself with a value computed from PYTHON_EXPRESSION"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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104 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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105 <param name="setdefinition_pythonexpression" type="text" label="Set sequence definition with a value computed" help="Use this option if you want to set sequence definition with a value computed from PYTHON_EXPRESSION"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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106 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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107 <param name="clearbool" type="boolean" label="Clear all attributes associated to the sequence records" truevalue="--clear" falsevalue="" help="Use this option if you want to clear all attributes associated to the sequence records" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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108 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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109 <section name="key_selector" title="Keep only attribute with key" expanded="False"> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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110 <param name="key" type="text" label="key" optional="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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111 <param name="key2" type="text" label="if you want to specify a second key" optional="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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112 <param name="key3" type="text" label="if you want to specify a third key" optional="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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113 <param name="key4" type="text" label="if you want to specify a fourth key" optional="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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114 <param name="key5" type="text" label="if you want to specify a fifth key" optional="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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115 </section> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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116 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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117 <param name="length" type="boolean" label="Use the length option?" truevalue="--length" falsevalue="" help="Use this option if you want to add attribute with seq_length as a key and sequence length as a value" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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118 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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119 <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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120 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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121 <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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122 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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123 <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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124 <expand macro="input_format_options_macro"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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125 <expand macro="out_format_macro"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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126 </inputs> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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127 <outputs> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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128 <data name="output" format="auto"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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129 </outputs> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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130 <tests> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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131 <test> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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132 <param name="input" value="output_obiuniq.fasta" ftype="fasta"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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133 <section name="key_selector"> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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134 <param name="key" value="count" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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135 <param name="key2" value="merged_sample" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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136 </section> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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137 <param name="uniqid" value="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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138 <param name="clearbool" value="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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139 <param name="length" value="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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140 <param name="seqrank" value="true" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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141 |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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142 <output name="output" file="output_obiannotate.fasta" ftype="fasta"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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143 </test> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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144 <test> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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145 <param name="input" value="output_obiuniq.fasta.gz" ftype="fasta.gz"/> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
1
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146 <section name="key_selector"> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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147 <param name="key" value="count" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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148 <param name="key2" value="merged_sample" /> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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149 </section> |
f82cefbbcea5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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150 <param name="uniqid" value="true" /> |
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151 <param name="clearbool" value="true" /> |
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152 <param name="length" value="true" /> |
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153 <param name="seqrank" value="true" /> |
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154 <output name="output" file="output_obiannotate.fasta.gz" ftype="fasta.gz" decompress="true"/> |
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155 </test> |
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156 <!-- TODO fastq input test --> |
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157 </tests> |
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158 |
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159 <help><![CDATA[ |
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160 |
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161 .. class:: infomark |
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162 |
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163 **What it does** |
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164 |
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165 `obiannotate` is the command that allows adding/modifying/removing annotation attributes attached to sequence records. |
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166 |
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167 Once such attributes are added, they can be used by the other OBITools commands for filtering purposes or for statistics computing. |
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168 |
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169 @OBITOOLS_LINK@ |
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170 |
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171 ]]> |
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172 |
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173 </help> |
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174 <expand macro="citation" /> |
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175 </tool> |