Mercurial > repos > iuc > kc_align

annotate kc-align.xml @ 4:a0ffbc759ad8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit aa22278999bbbda623372ab5f6dc701562624f6c"
author iuc
date Fri, 10 Apr 2020 13:55:47 -0400
parents 0243407479f1
children 1e70671a90c6
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a0ffbc759ad8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit aa22278999bbbda623372ab5f6dc701562624f6c"
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1 <tool id="kc-align" name="Kc-Align" version="0.1.5" python_template_version="3.5">
0
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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2 <requirements>
4
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3 <requirement type="package" version="0.5.13">kcalign</requirement>
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4 <requirement type="package" version="3.2.2">kalign3</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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8 kc-align
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9 --mode $position.mode
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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10 --reference '$reference'
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11 --reads '$reads'
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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12 #if $position.mode == "genome":
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13 --start $position.start
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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14 --end $position.end
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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15 #end if
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16 $compress
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17 ]]></command>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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18 <inputs>
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19 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
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20 <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
0
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21 <conditional name="position" >
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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22 <param name="mode" type="select" label="Mode" >
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23 <option value="genome">Genome</option>
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24 <option value="gene">Gene</option>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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25 <option value="mixed">Mixed</option>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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26 </param>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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27 <when value="genome" >
1
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28 <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" />
60ed1c94f584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit e87ad1b9f89ab8a1ccd5405de86d8e99901844c7"
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29 <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" />
0
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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30 </when>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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31 <when value="gene" >
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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32 </when>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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33 <when value="mixed" >
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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34 </when>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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35 </conditional>
2
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36 <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
0
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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37 </inputs>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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38 <outputs>
3
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39 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" />
0243407479f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 6c793b7cf264021bc72b96fbd9b6ceeefcb967bd"
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40 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${tool.name}: clustal output" />
0
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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41 </outputs>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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42 <tests>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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43 <test>
1
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44 <param name="reference" ftype="fasta" value="wuhan_ref.fasta" />
60ed1c94f584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit e87ad1b9f89ab8a1ccd5405de86d8e99901844c7"
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45 <param name="reads" ftype="fasta" value="3.fasta" />
0
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46 <param name="mode" value="genome" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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47 <param name="start" value="21563" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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48 <param name="end" value="25384" />
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49 <output name="fasta" ftype="fasta" compare="diff" value="kc-align.fasta" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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50 <output name="clustal" ftype="txt" compare="diff" value="kc-align.clustal" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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51 </test>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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52 </tests>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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53 <help><![CDATA[
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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54
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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55 ============
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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56 Kc-Align
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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57 ============
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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58
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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59 Kc-Algin is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces two outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format.
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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60
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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61 Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout.
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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62
1
60ed1c94f584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit e87ad1b9f89ab8a1ccd5405de86d8e99901844c7"
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63 Kc-Align also has functionality for genes that are are composed of more than one continuous sequence (currently only support for two segments). This can be achieved by entering each segments start coordinate in the Start Position parameter separated by a comma and then doing the same for each segments end coordinate in the End Position parameter (Ex: Start Postion: 12562,12591 End Position: 12592,13905)
60ed1c94f584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit e87ad1b9f89ab8a1ccd5405de86d8e99901844c7"
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64
0
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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65 Modes:
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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66 ------
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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67
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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68 Kc-Align can be run in three different modes, depending on your input data.
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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69
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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70 * In **genome** mode, the "reference" and "reads" input parameters are all full genome FASTA files. This mode also requires the 1-based start and end position numbers corresponding to the gene you are interested in aligning from the reference input.
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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71
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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72 * If both the "reference" and "reads" inputs are already in-frame genes, the **gene** mode should be used. This mode does not require start and end position parameters as the reference is already in-frame.
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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73
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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74 * For the case when your "reference" is an in-frame gene while the "reads" are whole genomes, the **mixed** mode can be used. Like gene mode, this mode does not require the start and end point position parameters.
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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75
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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76
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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77 ]]></help>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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78 <citations>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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79 <citation type="bibtex">
1
60ed1c94f584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit e87ad1b9f89ab8a1ccd5405de86d8e99901844c7"
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80 @misc{githubkcalign,
0
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81 author = {Nicholas Keener, Emil Bouvier},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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82 year = {2020},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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83 title = {Kc-Align},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
iuc
parents:
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84 publisher = {Github},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
iuc
parents:
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85 journal = {Github repository},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
iuc
parents:
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86 url = {https://github.com/davebx/kc-align},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
iuc
parents:
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87 }</citation>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
iuc
parents:
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88 </citations>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
iuc
parents:
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89 </tool>