Mercurial > repos > iuc > kc_align

annotate kc-align.xml @ 0:04b13fc809ac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
author iuc
date Tue, 17 Mar 2020 15:24:15 -0400
parents
children 60ed1c94f584
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04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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1 <tool id="kc-align" name="Kc-Align" version="0.1.0" python_template_version="3.5">
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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2 <requirements>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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3 <requirement type="package" version="0.5">kcalign</requirement>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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4 <requirement type="package" version="2.04">kalign2</requirement>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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5 </requirements>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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6 <command detect_errors="exit_code">
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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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
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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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'
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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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":
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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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
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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16 ]]></command>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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17 <inputs>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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18 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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19 <param name="reads" type="data" format="fasta" label="Reads" help="Single or multi-FASTA seqeunces to be aligned with the reference" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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20 <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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21 <param name="mode" type="select" label="Mode" >
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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22 <option value="genome">Genome</option>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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23 <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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24 <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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25 </param>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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26 <when value="genome" >
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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27 <param name="start" type="integer" value="0" min="0" label="Start Position" help="The 1-indexed start position of the gene of interest in the reference sequence" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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28 <param name="end" type="integer" value="0" min="0" label="End Position" help="The 1-indexed end position of the gene of interest in the reference sequence" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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29 </when>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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30 <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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31 </when>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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32 <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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33 </when>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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34 </conditional>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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35 </inputs>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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36 <outputs>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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37 <data name="fasta" format="fasta" from_work_dir="kc-align.fasta" label="out.fasta" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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38 <data name="clustal" format="txt" from_work_dir="kc-align.clustal" label="out.clustal" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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39 </outputs>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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40 <tests>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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41 <test>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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42 <param name="reference" ftype="fasta" value="MN908947.3.fasta" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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43 <param name="reads" ftype="fasta" value="corona.fasta" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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44 <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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45 <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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46 <param name="end" value="25384" />
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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47 <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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48 <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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49 </test>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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50 </tests>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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51 <help><![CDATA[
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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52
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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53 ============
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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54 Kc-Align
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
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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57 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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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-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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60
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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61 Modes:
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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62 ------
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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63
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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64 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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65
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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66 * 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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67
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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68 * 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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69
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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70 * 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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71
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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72
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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73 ]]></help>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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74 <citations>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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75 <citation type="bibtex">
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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76 @misc{githubkcalign,
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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77 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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78 year = {2020},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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79 title = {Kc-Align},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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80 publisher = {Github},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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81 journal = {Github repository},
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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82 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"
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83 }</citation>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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84 </citations>
04b13fc809ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
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85 </tool>