Mercurial > repos > iuc > obi_convert
annotate macros.xml @ 4:e328ced6cf0a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author | iuc |
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date | Wed, 20 Mar 2024 13:15:46 +0000 |
parents | 374fd9feb032 |
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rev | line source |
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0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
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1 <?xml version="1.0"?> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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2 <macros> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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3 <xml name="requirements"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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4 <requirements> |
1
6259965de501
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents:
0
diff
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5 <requirement type="package" version="@TOOL_VERSION@">obitools</requirement> |
0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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6 </requirements> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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7 </xml> |
4
e328ced6cf0a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents:
3
diff
changeset
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8 <xml name="bio_tools"> |
e328ced6cf0a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents:
3
diff
changeset
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9 <xrefs> |
e328ced6cf0a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents:
3
diff
changeset
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10 <xref type="bio.tools">obitools</xref> |
e328ced6cf0a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents:
3
diff
changeset
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11 </xrefs> |
e328ced6cf0a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents:
3
diff
changeset
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12 </xml> |
3
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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changeset
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13 <token name="@TOOL_VERSION@">1.2.13</token> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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changeset
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14 <token name="@PROFILE@">21.01</token> |
0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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15 |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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16 <xml name="stdio"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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17 <stdio> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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18 <exit_code range="1:" level="fatal" description="Error in Obitools execution" /> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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19 </stdio> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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20 </xml> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
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21 |
3
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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changeset
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22 <token name="@INPUT_FORMATS@">fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz</token> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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23 <token name="@GUNZIP_INPUT@"><![CDATA[ |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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24 #if $input.ext.endswith(".gz") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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25 gunzip -c '$input' > input && |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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26 #else |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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27 ln -s '$input' input && |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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28 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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29 ]]></token> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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30 <token name="@GZIP_OUTPUT@"><![CDATA[ |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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31 #if $input.ext.endswith(".gz") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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changeset
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32 | gzip -c |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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33 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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34 ]]></token> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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35 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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36 <!-- generate galaxy.json to determine output format |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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37 - by default same as input |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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38 - if out_format can be specified |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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39 - fasta/fastq depending on $out_format (if != "") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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40 - or fasta if the tool does not support choosing the output format, e.g. obiuniq which always outputs fasta |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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41 - gz if $input is zipped |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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42 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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43 A list of outputs to include in the json can be given by |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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44 setting a variable $outputs = [...] listing pairs of output names and the actual output |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
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45 (defaults to [("output", $output)]) |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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46 --> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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47 <token name="@GENERATE_GALAXY_JSON@"><![CDATA[ |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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changeset
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48 #import json |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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49 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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50 #try: |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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51 #silent $outputs[0] |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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52 #except |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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53 #set outputs = [("output", $output)] |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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54 #end try |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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55 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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56 #if $input.ext.startswith("fastq") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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57 #set ext = "fastqsanger" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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58 #else if $input.ext.startswith("fasta") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
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59 #set ext = "fasta" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
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60 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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61 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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62 #try |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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63 #if $out_format == "fasta" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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64 #set ext = "fasta" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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65 #else if $out_format == "fastq" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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66 #set ext = "fastqsanger" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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67 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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68 #except |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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69 #set ext = "fasta" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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70 #end try |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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71 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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72 #if $input.ext.endswith(".gz") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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73 #set ext = ext + ".gz" |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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74 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
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75 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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76 #set gxy_json = {} |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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77 #for oname, o in $outputs |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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78 #silent gxy_json[oname] = {"ext": ext} |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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79 #end for |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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80 && echo '${json.dumps(gxy_json)}' >> galaxy.json |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
81 ]]></token> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
82 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
83 <token name="@OUT_FORMAT@"><![CDATA[ |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
84 #if $out_format |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
85 --${out_format}-output |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
86 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
87 ]]></token> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
88 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
89 <xml name="out_format_macro"> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
90 <param name="out_format" type="select" optional="true" label="Output data type" help="For FASTA/Q the the default output type is the same as the input type"> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
91 <option value="fasta">fasta</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
92 <option value="fastq">fastq</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
93 </param> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
94 </xml> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
2
diff
changeset
|
95 |
0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
96 <token name="@OBITOOLS_LINK@"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
97 <![CDATA[ |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
98 -------- |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
99 |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
100 **Project links:** |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
101 |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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changeset
|
102 `OBITools`_ |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
103 |
2
4d705e3443a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents:
1
diff
changeset
|
104 .. _OBITools: https://pythonhosted.org/OBITools/ |
0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
105 ]]> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
106 </token> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
107 |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
108 <xml name="attributes"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
109 <option value="ali_dir" selected="true">ali_dir</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
110 <option value="ali_length">ali_length</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
111 <option value="avg_quality">avg_quality</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
112 <option value="best_match">best_match</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
113 <option value="best_identity">best_identity</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
114 <option value="class">class</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
115 <option value="cluster">cluster</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
116 <option value="complemented">complemented</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
117 <option value="count">count</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
118 <option value="cut">cut</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
119 <option value="direction">direction</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
120 <option value="distance">distance</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
121 <option value="error">error</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
122 <option value="experiment">experiment</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
123 <option value="family">family</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
124 <option value="family_name">family_name</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
125 <option value="forward_error">forward_error</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
126 <option value="forward_match">forward_match</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
127 <option value="forward_primer">forward_primer</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
128 <option value="forward_score">forward_score</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
129 <option value="forward_tag">forward_tag</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
130 <option value="forward_tm">forward_tm</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
131 <option value="genus">genus</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
132 <option value="genus_name">genus_name</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
133 <option value="head_quality">head_quality</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
134 <option value="id_status">id_status</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
135 <option value="merged_star">merged_star</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
136 <option value="merged">merged</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
137 <option value="mid_quality">mid_quality</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
138 <option value="mode">mode</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
139 <option value="obiclean_cluster">obiclean_cluster</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
140 <option value="obiclean_count">obiclean_count</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
141 <option value="obiclean_head">obiclean_head</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
142 <option value="obiclean_headcount">obiclean_headcount</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
143 <option value="obiclean_internalcount">obiclean_internalcount</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
144 <option value="obiclean_samplecount">obiclean_samplecount</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
145 <option value="obiclean_singletoncount">obiclean_singletoncount</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
146 <option value="obiclean_status">obiclean_status</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
147 <option value="occurrence">occurrence</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
148 <option value="order">order</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
149 <option value="order_name">order_name</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
150 <option value="pairend_limit ">pairend_limit </option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
151 <option value="partial ">partial </option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
152 <option value="rank">rank</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
153 <option value="reverse_error">reverse_error</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
154 <option value="reverse_match">reverse_match</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
155 <option value="reverse_primer">reverse_primer</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
156 <option value="reverse_score">reverse_score</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
157 <option value="reverse_tag">reverse_tag</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
158 <option value="reverse_tm">reverse_tm</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
159 <option value="sample">sample</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
160 <option value="scientific_name">scientific_name</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
161 <option value="score">score</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff
changeset
|
162 <option value="score_norm">score_norm</option> |
93f8e0553bcd
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163 <option value="select">select</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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164 <option value="seq_ab_match">seq_ab_match</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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165 <option value="seq_a_single">seq_a_single</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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166 <option value="seq_a_mismatch">seq_a_mismatch</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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167 <option value="seq_a_deletion">seq_a_deletion</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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168 <option value="seq_a_insertion">seq_a_insertion</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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169 <option value="seq_b_single">seq_b_single</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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170 <option value="seq_b_mismatch">seq_b_mismatch</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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171 <option value="seq_b_deletion">seq_b_deletion</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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172 <option value="seq_b_insertion">seq_b_insertion</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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173 <option value="seq_length">seq_length</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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174 <option value="seq_length_ori">seq_length_ori</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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175 <option value="seq_rank">seq_rank</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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176 <option value="sminL">sminL</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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177 <option value="sminR">sminR</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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178 <option value="species">species</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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179 <option value="species_list">species_list</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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180 <option value="species_name">species_name</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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181 <option value="status">status</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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182 <option value="strand">strand</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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183 <option value="tail_quality">tail_quality</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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184 <option value="taxid">taxid</option> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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185 </xml> |
93f8e0553bcd
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186 |
3
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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187 <xml name="input_format_options_macro"> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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188 <section name="input_format_options" title="Input format options" expanded="false"> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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189 <param name="options_inputtype" type="select" optional="true" label="Specify the input datatype" help="default: determine automatically (should only be necessay for non FASTA/FASTQ datasets)"> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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190 <option value="--genbank">genbank</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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191 <option value="--embl">embl</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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192 <option value="--sanger">sanger</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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193 <option value="--solexa">solexa</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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194 <option value="--ecopcr">ecopcr</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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195 <option value="--ecopcrdb">ecopcrdb</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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196 <option value="--fasta">fasta (including obitools fasta extentions)</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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197 <option value="--raw-fasta">raw fasta (more tolerant format variant)</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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198 </param> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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199 <param name="options_seqtype" type="select" optional="true" label="Specify the sequence datatype" > |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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200 <option value="--nuc">nucleic</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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201 <option value="--prot">protein</option> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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202 </param> |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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203 </section> |
0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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204 </xml> |
3
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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205 |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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206 <token name="@INPUT_FORMAT@"><![CDATA[ |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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207 #if $input_format_options.options_inputtype |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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208 $input_format_options.options_inputtype |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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209 #else |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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210 #if $input.ext.startswith("fasta") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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211 --fasta |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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212 #else if $input.ext.startswith("fastqsolexa") |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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213 ## input file is in fastq nucleic format produced by solexa sequencer |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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214 --solexa |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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215 #else |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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216 ## input file is in sanger fastq nucleic format (standard fastq) |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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217 --sanger |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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218 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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219 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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220 #if $input_format_options.options_seqtype |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents:
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221 $input_format_options.options_seqtype |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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222 #end if |
374fd9feb032
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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223 ]]></token> |
0
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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224 |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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225 <xml name="sanitizer"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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226 <sanitizer invalid_char="test"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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227 <valid initial="default"> |
93f8e0553bcd
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iuc
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228 <!--add value="""/--> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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229 </valid> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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230 <mapping initial="default"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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231 <add source=">" target="\>"/> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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232 <add source=""" target="\""/> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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233 </mapping> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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234 </sanitizer> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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235 </xml> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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236 |
93f8e0553bcd
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iuc
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237 <xml name="citation"> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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|
238 <citations> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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239 <citation type="doi">10.1111/1755-0998.12428</citation> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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|
240 </citations> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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241 </xml> |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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242 |
93f8e0553bcd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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243 </macros> |