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annotate macros.xml.orig @ 4:d5d44f7d6e4a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:50:49 +0000
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4
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
1 <?xml version="1.0"?>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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2 <macros>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <xml name="requirements">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <requirements>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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6 </requirements>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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7 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 <<<<<<< HEAD
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <token name="@TOOL_VERSION@">1.2.13</token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 <token name="@PROFILE@">21.01</token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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12 =======
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 <xml name="bio_tools">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 <xrefs>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 <xref type='bio.tools'>obitools</xref>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 </xrefs>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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17 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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18 <token name="@TOOL_VERSION@">1.2.11</token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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19 >>>>>>> 7abad681f (add tools up until P)
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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21 <xml name="stdio">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 <stdio>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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23 <exit_code range="1:" level="fatal" description="Error in Obitools execution" />
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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24 </stdio>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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25 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27 <token name="@INPUT_FORMATS@">fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz</token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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28 <token name="@GUNZIP_INPUT@"><![CDATA[
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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29 #if $input.ext.endswith(".gz")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 gunzip -c '$input' > input &&
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 #else
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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32 ln -s '$input' input &&
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34 ]]></token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 <token name="@GZIP_OUTPUT@"><![CDATA[
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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36 #if $input.ext.endswith(".gz")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 | gzip -c
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 ]]></token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 <!-- generate galaxy.json to determine output format
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 - by default same as input
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43 - if out_format can be specified
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44 - fasta/fastq depending on $out_format (if != "")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 - or fasta if the tool does not support choosing the output format, e.g. obiuniq which always outputs fasta
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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46 - gz if $input is zipped
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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47
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 A list of outputs to include in the json can be given by
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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49 setting a variable $outputs = [...] listing pairs of output names and the actual output
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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50 (defaults to [("output", $output)])
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 -->
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52 <token name="@GENERATE_GALAXY_JSON@"><![CDATA[
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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53 #import json
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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54
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 #try:
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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56 #silent $outputs[0]
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 #except
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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58 #set outputs = [("output", $output)]
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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59 #end try
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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60
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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61 #if $input.ext.startswith("fastq")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62 #set ext = "fastqsanger"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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63 #else if $input.ext.startswith("fasta")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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64 #set ext = "fasta"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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66
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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67 #try
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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68 #if $out_format == "fasta"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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69 #set ext = "fasta"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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70 #else if $out_format == "fastq"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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71 #set ext = "fastqsanger"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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72 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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73 #except
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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74 #set ext = "fasta"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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75 #end try
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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76
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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77 #if $input.ext.endswith(".gz")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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78 #set ext = ext + ".gz"
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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79 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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80
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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81 #set gxy_json = {}
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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82 #for oname, o in $outputs
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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83 #silent gxy_json[oname] = {"ext": ext}
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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84 #end for
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
85 && echo '${json.dumps(gxy_json)}' >> galaxy.json
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
86 ]]></token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
87
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
88 <token name="@OUT_FORMAT@"><![CDATA[
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
89 #if $out_format
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
90 --${out_format}-output
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
91 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
92 ]]></token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
93
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
94 <xml name="out_format_macro">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
95 <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">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
96 <option value="fasta">fasta</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
97 <option value="fastq">fastq</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
98 </param>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
99 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
100
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
101 <token name="@OBITOOLS_LINK@">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
102 <![CDATA[
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
103 --------
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
104
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
105 **Project links:**
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
106
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
107 `OBITools`_
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
108
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
109 .. _OBITools: https://pythonhosted.org/OBITools/
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
110 ]]>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
111 </token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
112
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
113 <xml name="attributes">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
114 <option value="ali_dir" selected="true">ali_dir</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
115 <option value="ali_length">ali_length</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
116 <option value="avg_quality">avg_quality</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
117 <option value="best_match">best_match</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
118 <option value="best_identity">best_identity</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
119 <option value="class">class</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
120 <option value="cluster">cluster</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
121 <option value="complemented">complemented</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
122 <option value="count">count</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
123 <option value="cut">cut</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
124 <option value="direction">direction</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
125 <option value="distance">distance</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
126 <option value="error">error</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
127 <option value="experiment">experiment</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
128 <option value="family">family</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
129 <option value="family_name">family_name</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
130 <option value="forward_error">forward_error</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
131 <option value="forward_match">forward_match</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
132 <option value="forward_primer">forward_primer</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
133 <option value="forward_score">forward_score</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
134 <option value="forward_tag">forward_tag</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
135 <option value="forward_tm">forward_tm</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
136 <option value="genus">genus</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
137 <option value="genus_name">genus_name</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
138 <option value="head_quality">head_quality</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
139 <option value="id_status">id_status</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
140 <option value="merged_star">merged_star</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
141 <option value="merged">merged</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
142 <option value="mid_quality">mid_quality</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
143 <option value="mode">mode</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
144 <option value="obiclean_cluster">obiclean_cluster</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
145 <option value="obiclean_count">obiclean_count</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
146 <option value="obiclean_head">obiclean_head</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
147 <option value="obiclean_headcount">obiclean_headcount</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
148 <option value="obiclean_internalcount">obiclean_internalcount</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
149 <option value="obiclean_samplecount">obiclean_samplecount</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
150 <option value="obiclean_singletoncount">obiclean_singletoncount</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
151 <option value="obiclean_status">obiclean_status</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
152 <option value="occurrence">occurrence</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
153 <option value="order">order</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
154 <option value="order_name">order_name</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
155 <option value="pairend_limit ">pairend_limit </option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
156 <option value="partial ">partial </option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
157 <option value="rank">rank</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
158 <option value="reverse_error">reverse_error</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
159 <option value="reverse_match">reverse_match</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
160 <option value="reverse_primer">reverse_primer</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
161 <option value="reverse_score">reverse_score</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
162 <option value="reverse_tag">reverse_tag</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
163 <option value="reverse_tm">reverse_tm</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
164 <option value="sample">sample</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
165 <option value="scientific_name">scientific_name</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
166 <option value="score">score</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
167 <option value="score_norm">score_norm</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
168 <option value="select">select</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
169 <option value="seq_ab_match">seq_ab_match</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
170 <option value="seq_a_single">seq_a_single</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
171 <option value="seq_a_mismatch">seq_a_mismatch</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
172 <option value="seq_a_deletion">seq_a_deletion</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
173 <option value="seq_a_insertion">seq_a_insertion</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
174 <option value="seq_b_single">seq_b_single</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
175 <option value="seq_b_mismatch">seq_b_mismatch</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
176 <option value="seq_b_deletion">seq_b_deletion</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
177 <option value="seq_b_insertion">seq_b_insertion</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
178 <option value="seq_length">seq_length</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
179 <option value="seq_length_ori">seq_length_ori</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
180 <option value="seq_rank">seq_rank</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
181 <option value="sminL">sminL</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
182 <option value="sminR">sminR</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
183 <option value="species">species</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
184 <option value="species_list">species_list</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
185 <option value="species_name">species_name</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
186 <option value="status">status</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
187 <option value="strand">strand</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
188 <option value="tail_quality">tail_quality</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
189 <option value="taxid">taxid</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
190 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
191
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
192 <xml name="input_format_options_macro">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
193 <section name="input_format_options" title="Input format options" expanded="false">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
194 <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)">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
195 <option value="--genbank">genbank</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
196 <option value="--embl">embl</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
197 <option value="--sanger">sanger</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
198 <option value="--solexa">solexa</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
199 <option value="--ecopcr">ecopcr</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
200 <option value="--ecopcrdb">ecopcrdb</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
201 <option value="--fasta">fasta (including obitools fasta extentions)</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
202 <option value="--raw-fasta">raw fasta (more tolerant format variant)</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
203 </param>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
204 <param name="options_seqtype" type="select" optional="true" label="Specify the sequence datatype" >
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
205 <option value="--nuc">nucleic</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
206 <option value="--prot">protein</option>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
207 </param>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
208 </section>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
209 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
210
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
211 <token name="@INPUT_FORMAT@"><![CDATA[
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
212 #if $input_format_options.options_inputtype
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
213 $input_format_options.options_inputtype
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
214 #else
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
215 #if $input.ext.startswith("fasta")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
216 --fasta
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
217 #else if $input.ext.startswith("fastqsolexa")
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
218 ## input file is in fastq nucleic format produced by solexa sequencer
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
219 --solexa
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
220 #else
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
221 ## input file is in sanger fastq nucleic format (standard fastq)
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
222 --sanger
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
223 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
224 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
225 #if $input_format_options.options_seqtype
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
226 $input_format_options.options_seqtype
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
227 #end if
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
228 ]]></token>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
229
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
230 <xml name="sanitizer">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
231 <sanitizer invalid_char="test">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
232 <valid initial="default">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
233 <!--add value="&quot;"/-->
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
234 </valid>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
235 <mapping initial="default">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
236 <add source="&gt;" target="\&gt;"/>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
237 <add source="&quot;" target="\&quot;"/>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
238 </mapping>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
239 </sanitizer>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
240 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
241
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
242 <xml name="citation">
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
243 <citations>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
244 <citation type="doi">10.1111/1755-0998.12428</citation>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
245 </citations>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
246 </xml>
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
247
d5d44f7d6e4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
248 </macros>