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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit 75a9dab06b5d4cec61475c2ba0d77fc21bd95dfc"
author iuc
date Tue, 04 Jan 2022 16:48:54 +0000
parents 03b9fd82cf30
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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1 <tool id="minia" name="Minia" version="@TOOL_VERSION@">
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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2 <description>Short-read assembler based on a de Bruijn graph</description>
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553cf3df936c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
553cf3df936c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">minia</xref>
553cf3df936c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
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8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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6 <macros>
3
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7 <token name="@TOOL_VERSION@">3.2.6</token>
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8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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8 </macros>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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9 <requirements>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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10 <requirement type="package" version="@TOOL_VERSION@">minia</requirement>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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11 </requirements>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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12 <command detect_errors="exit_code"><![CDATA[
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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13 #set input = 'infile.' + $in.ext
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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14 ln -s '$in' '$input' &&
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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15
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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16 minia
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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17 -in '$input'
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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18 -kmer-size $kmer_size
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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19 #if str($abundance_min):
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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20 -abundance-min $abundance_min
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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21 #end if
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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22 #if str($abundance_max):
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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23 -abundance-min $abundance_max
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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24 #end if
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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25 -nb-cores \${GALAXY_SLOTS:-1}
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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26 -out output
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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27 ]]></command>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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28 <inputs>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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29 <param argument="-in" type="data" format="fasta,fastqsanger,fastqsanger.gz,fasta.gz" label="Reads in FASTA or FASTQ format" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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30 <param argument="-kmer-size" type="integer" value="31" min="1" label="Size of a kmer" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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31 <param argument="-abundance-min" type="integer" value="" optional="true" min="0" label="Min abundance threshold for solid kmers (default: 2)" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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32 <param argument="-abundance-max" type="integer" value="" optional="true" label="Max abundance threshold for solid kmers" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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33 </inputs>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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34 <outputs>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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35 <data name="output" format="fasta" label="${tool.name} on ${on_string}" from_work_dir="output.contigs.fa" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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36 </outputs>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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37 <tests>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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38 <test>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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39 <param name="in" value="ec.fa" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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40 <param name="kmer_size" value="21" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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41 <param name="abundance_min" value="1" />
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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42 <output name="output" ftype="fasta">
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43 <assert_contents>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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44 <has_text text="LN:i:460 KC:i:2200 km:f:5.000"/>
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45 <has_text text="LN:i:637 KC:i:3085 km:f:5.000"/>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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46 <has_n_lines n="4"/>
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47 </assert_contents>
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48 </output>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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49 </test>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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50 </tests>
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51 <help><![CDATA[
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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52 Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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53 The output of Minia is a set of contigs.
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54 ]]></help>
8a6ff5a83a29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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55 <citations>
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56 <citation type="doi">10.1186/1748-7188-8-22</citation>
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57 </citations>
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58 </tool>