Mercurial > repos > iuc > mykrobe_genotype

annotate macro.xml @ 2:0f4a5de7878a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 65f9e423263afc8f23fa51cb4770998b99f933ba"
author iuc
date Thu, 02 Jan 2020 12:04:06 -0500
parents 84f769706f7a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
0f4a5de7878a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 65f9e423263afc8f23fa51cb4770998b99f933ba"
iuc
parents: 1
diff changeset
1 <?xml version="1.1"?>
0
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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2 <macros>
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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3 <xml name="requirements">
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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4 <requirements>
2
0f4a5de7878a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 65f9e423263afc8f23fa51cb4770998b99f933ba"
iuc
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5 <requirement type="package" version="0.7.0">mykrobe</requirement>
0
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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6 </requirements>
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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7 </xml>
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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8 <token name="@select_inputs@">
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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9 <![CDATA[
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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10 #set $name='sample'
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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11 #set $type='fastq'
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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12 ## Adding sample name, indicate specie and inputs fastq(s) files
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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13 #if $data_type.type == "paired":
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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14
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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15 ln -s '$data_type.fastq_input1' sample_1.fastq &&
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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16 ln -s '$data_type.fastq_input2' sample_2.fastq &&
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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17
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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18
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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19 #elif $data_type.type == "collection":
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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20 #set $name=str($data_type.fastq_input1.name)
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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21 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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22 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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23
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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24 #elif $data_type.type == "single":
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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26
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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27 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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28 ln -s '$data_type.fastq_input1' sample.fastq &&
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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29
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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30 #end if
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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31
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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32 #if $data_type.fastq_input1.is_of_type('bam'):
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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33 ln -s '$data_type.fastq_input1' sample.bam &&
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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34 #set $type='bam'
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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35 #end if
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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36
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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37 #end if
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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38 ]]>
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
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39 </token>
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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40
1
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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41 <token name="@shared_options@">
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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42 <![CDATA[
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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43 #if $kmer:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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44 --kmer '${kmer}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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45 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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46 #if $expected_depth:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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47 --expected_depth '${expected_depth}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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48 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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49
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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50 $ont
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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51
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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52 $report_all_calls
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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54 #if $expected_error_rate:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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55 --expected_error_rate '${expected_error_rate}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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56 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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57
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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58 #if $min_variant_conf:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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59 --min_variant_conf '${min_variant_conf}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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60 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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62 #if $min_gene_conf:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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63 --min_gene_conf '${min_gene_conf}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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64 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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66 #if $min_proportion_expected_depth:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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67 --min_proportion_expected_depth '${min_proportion_expected_depth}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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68 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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69
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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70 #if $min_gene_percent_covg_threshold:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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71 --min_gene_percent_covg_threshold '${min_gene_percent_covg_threshold}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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72 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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74 $guess_sequence_method
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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76 $ignore_minor_calls
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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78 #if $ignore_filtered:
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79 --ignore_filtered '${ignore_filtered}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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80 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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82 #if $model:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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83 --model '${model}'
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84 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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86 #if $ploidy:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
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87 --ploidy '${ploidy}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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88 #end if
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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89 ]]>
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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90 </token>
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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91
0
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92 <xml name="inputs">
d783eb846f59 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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93 <conditional name="data_type">
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94 <param name="type" type="select" label="Specify the read type.">
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95 <option value="single">Single-end Data</option>
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96 <option value="paired">Paired-end Data</option>
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97 <option value="collection">Collection Paired-end Data</option>
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98 </param>
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99 <when value="single">
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100 <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
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101 </when>
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102 <when value="paired">
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103 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
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104 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
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105 </when>
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106 <when value="collection">
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107 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
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108 </when>
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109 </conditional>
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110 </xml>
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111
1
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112 <xml name="options">
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113 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
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114 <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate" help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
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115 <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>
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116 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
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117 <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
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118 <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>
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119 <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage" help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/>
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120 <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
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121 <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
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122 <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
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123 <option value="diploid">diploid</option>
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124 <option value="haploid">haploid</option>
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125 </param>
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126 <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>
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127 <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>
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128 <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
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129 <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method" help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
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130 </xml>
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131
0
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132 <token name="@ATTRIBUTION@">
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133 <![CDATA[
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134
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135 **MyKrobe predict - Antibiotic resistance predictions**
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136
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137 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
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138 using Bruijn graph.
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139 ]]>
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140 </token>
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141
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142 <xml name="citation">
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143 <citations>
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144 <citation type="doi">10.1038/ncomms10063</citation>
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145 </citations>
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146 </xml>
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147 </macros>