Mercurial > repos > iuc > minia

annotate minia.xml @ 0:0a66ef6dacb7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
author iuc
date Thu, 09 Apr 2020 03:42:24 -0400
parents
children b2dc51639ad5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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1 <tool id="minia" name="Minia" version="@TOOL_VERSION@">
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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2 <description>Short-read assembler based on a de Bruijn graph</description>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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3 <macros>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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4 <token name="@TOOL_VERSION@">3.2.1</token>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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5 </macros>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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6 <requirements>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">minia</requirement>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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8 </requirements>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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9 <command detect_errors="exit_code"><![CDATA[
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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10 #set input = 'infile.' + $in.ext
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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11 ln -s '$in' '$input' &&
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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12
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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13 minia
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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14 -in '$input'
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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15 -kmer-size $kmer_size
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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16 #if str($abundance_min):
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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17 -abundance-min $abundance_min
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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18 #end if
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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19 #if str($abundance_max):
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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20 -abundance-min $abundance_max
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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21 #end if
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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22 -nb-cores \${GALAXY_SLOTS:-1}
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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23 -out output
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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24 ]]></command>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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25 <inputs>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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26 <param argument="-in" type="data" format="fasta,fastqsanger,fastqsanger.gz,fasta.gz" label="Reads in FASTA or FASTQ format" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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27 <param argument="-kmer-size" type="integer" value="31" min="1" label="Size of a kmer" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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28 <param argument="-abundance-min" type="integer" value="" optional="true" min="0" label="Min abundance threshold for solid kmers (default: 2)" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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29 <param argument="-abundance-max" type="integer" value="" optional="true" label="Max abundance threshold for solid kmers" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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30 </inputs>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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31 <outputs>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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32 <data name="output" format="fasta" label="${tool.name} on ${on_string}" from_work_dir="output.contigs.fa" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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33 </outputs>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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34 <tests>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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35 <test>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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36 <param name="in" value="ec.fa" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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37 <param name="kmer_size" value="21" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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38 <param name="abundance_min" value="1" />
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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39 <output name="output" ftype="fasta">
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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40 <assert_contents>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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41 <has_text text="LN:i:460 KC:i:2200 km:f:5.000"/>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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42 <has_text text="LN:i:637 KC:i:3085 km:f:5.000"/>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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43 <has_n_lines n="4"/>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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44 </assert_contents>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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45 </output>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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46 </test>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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47 </tests>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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48 <help><![CDATA[
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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49 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.
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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50 The output of Minia is a set of contigs.
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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51 ]]></help>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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52 <citations>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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53 <citation type="doi">10.1186/1748-7188-8-22</citation>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
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54 </citations>
0a66ef6dacb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
iuc
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55 </tool>