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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:15:59 +0000
parents e614dcabd870
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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1 <?xml version="1.0"?>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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2 <macros>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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3 <xml name="requirements">
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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4 <requirements>
1
0de27b538106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
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5 <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
0
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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6 </requirements>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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7 </xml>
4
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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8 <xml name="bio_tools">
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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9 <xrefs>
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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10 <xref type="bio.tools">obitools</xref>
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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11 </xrefs>
b6d9ea2fb41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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12 </xml>
3
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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13 <token name="@TOOL_VERSION@">1.2.13</token>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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14 <token name="@PROFILE@">21.01</token>
0
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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16 <xml name="stdio">
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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17 <stdio>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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18 <exit_code range="1:" level="fatal" description="Error in Obitools execution" />
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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19 </stdio>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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20 </xml>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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21
3
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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22 <token name="@INPUT_FORMATS@">fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz</token>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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23 <token name="@GUNZIP_INPUT@"><![CDATA[
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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24 #if $input.ext.endswith(".gz")
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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25 gunzip -c '$input' > input &&
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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26 #else
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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27 ln -s '$input' input &&
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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28 #end if
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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29 ]]></token>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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30 <token name="@GZIP_OUTPUT@"><![CDATA[
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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31 #if $input.ext.endswith(".gz")
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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32 | gzip -c
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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33 #end if
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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34 ]]></token>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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35
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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36 <!-- generate galaxy.json to determine output format
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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37 - by default same as input
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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38 - if out_format can be specified
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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39 - fasta/fastq depending on $out_format (if != "")
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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40 - or fasta if the tool does not support choosing the output format, e.g. obiuniq which always outputs fasta
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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41 - gz if $input is zipped
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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42
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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43 A list of outputs to include in the json can be given by
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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44 setting a variable $outputs = [...] listing pairs of output names and the actual output
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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45 (defaults to [("output", $output)])
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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46 -->
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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47 <token name="@GENERATE_GALAXY_JSON@"><![CDATA[
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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48 #import json
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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49
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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50 #try:
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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51 #silent $outputs[0]
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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52 #except
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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53 #set outputs = [("output", $output)]
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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54 #end try
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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55
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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56 #if $input.ext.startswith("fastq")
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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57 #set ext = "fastqsanger"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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58 #else if $input.ext.startswith("fasta")
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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59 #set ext = "fasta"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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60 #end if
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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61
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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62 #try
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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63 #if $out_format == "fasta"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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64 #set ext = "fasta"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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65 #else if $out_format == "fastq"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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66 #set ext = "fastqsanger"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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67 #end if
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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68 #except
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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69 #set ext = "fasta"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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70 #end try
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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71
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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72 #if $input.ext.endswith(".gz")
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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73 #set ext = ext + ".gz"
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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74 #end if
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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75
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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76 #set gxy_json = {}
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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77 #for oname, o in $outputs
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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78 #silent gxy_json[oname] = {"ext": ext}
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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79 #end for
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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80 && echo '${json.dumps(gxy_json)}' >> galaxy.json
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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81 ]]></token>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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82
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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83 <token name="@OUT_FORMAT@"><![CDATA[
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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84 #if $out_format
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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85 --${out_format}-output
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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86 #end if
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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87 ]]></token>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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88
e614dcabd870 "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">
e614dcabd870 "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">
e614dcabd870 "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>
e614dcabd870 "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>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
93 </param>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
94 </xml>
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
95
0
aca6a8c9cf83 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@">
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
97 <![CDATA[
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
98 --------
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
99
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
100 **Project links:**
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
101
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
102 `OBITools`_
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
103
2
12b9e285ca1c "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
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
105 ]]>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
106 </token>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
107
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
108 <xml name="attributes">
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 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>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
163 <option value="select">select</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
164 <option value="seq_ab_match">seq_ab_match</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
165 <option value="seq_a_single">seq_a_single</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
166 <option value="seq_a_mismatch">seq_a_mismatch</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
167 <option value="seq_a_deletion">seq_a_deletion</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
168 <option value="seq_a_insertion">seq_a_insertion</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
169 <option value="seq_b_single">seq_b_single</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
170 <option value="seq_b_mismatch">seq_b_mismatch</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
171 <option value="seq_b_deletion">seq_b_deletion</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
172 <option value="seq_b_insertion">seq_b_insertion</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
173 <option value="seq_length">seq_length</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
174 <option value="seq_length_ori">seq_length_ori</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
175 <option value="seq_rank">seq_rank</option>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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176 <option value="sminL">sminL</option>
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177 <option value="sminR">sminR</option>
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178 <option value="species">species</option>
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179 <option value="species_list">species_list</option>
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180 <option value="species_name">species_name</option>
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181 <option value="status">status</option>
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182 <option value="strand">strand</option>
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183 <option value="tail_quality">tail_quality</option>
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184 <option value="taxid">taxid</option>
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185 </xml>
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186
3
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187 <xml name="input_format_options_macro">
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188 <section name="input_format_options" title="Input format options" expanded="false">
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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)">
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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190 <option value="--genbank">genbank</option>
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191 <option value="--embl">embl</option>
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192 <option value="--sanger">sanger</option>
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193 <option value="--solexa">solexa</option>
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194 <option value="--ecopcr">ecopcr</option>
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195 <option value="--ecopcrdb">ecopcrdb</option>
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196 <option value="--fasta">fasta (including obitools fasta extentions)</option>
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197 <option value="--raw-fasta">raw fasta (more tolerant format variant)</option>
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198 </param>
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199 <param name="options_seqtype" type="select" optional="true" label="Specify the sequence datatype" >
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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200 <option value="--nuc">nucleic</option>
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201 <option value="--prot">protein</option>
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202 </param>
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203 </section>
0
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204 </xml>
3
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205
e614dcabd870 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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206 <token name="@INPUT_FORMAT@"><![CDATA[
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207 #if $input_format_options.options_inputtype
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208 $input_format_options.options_inputtype
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209 #else
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210 #if $input.ext.startswith("fasta")
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211 --fasta
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212 #else if $input.ext.startswith("fastqsolexa")
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213 ## input file is in fastq nucleic format produced by solexa sequencer
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214 --solexa
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215 #else
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216 ## input file is in sanger fastq nucleic format (standard fastq)
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217 --sanger
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218 #end if
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219 #end if
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220 #if $input_format_options.options_seqtype
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221 $input_format_options.options_seqtype
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222 #end if
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223 ]]></token>
0
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224
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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225 <xml name="sanitizer">
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226 <sanitizer invalid_char="test">
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227 <valid initial="default">
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228 <!--add value="&quot;"/-->
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229 </valid>
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230 <mapping initial="default">
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231 <add source="&gt;" target="\&gt;"/>
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232 <add source="&quot;" target="\&quot;"/>
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233 </mapping>
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234 </sanitizer>
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235 </xml>
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236
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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237 <xml name="citation">
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238 <citations>
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239 <citation type="doi">10.1111/1755-0998.12428</citation>
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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240 </citations>
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241 </xml>
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242
aca6a8c9cf83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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243 </macros>