Mercurial > repos > iuc > spades_metaplasmidspades
annotate metaplasmidspades.xml @ 7:e5a3b75a271f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
author | iuc |
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date | Tue, 23 Aug 2022 08:01:19 +0000 |
parents | 4a01e0d2892c |
children | 037f9927c4ff |
rev | line source |
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0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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1 <tool id="spades_metaplasmidspades" name="metaplasmidSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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2 <description>extract and assembly plasmids from metagenomic data</description> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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3 <macros> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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4 <import>macros.xml</import> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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5 </macros> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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6 <expand macro="requirements"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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7 <expand macro="stdio"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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8 <expand macro="version_command"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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9 <command detect_errors="exit_code"><![CDATA[ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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10 |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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11 #set $library = 1 |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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12 |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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13 @PREPROCESS_INPUT_FILES_MAIN@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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14 #if $additional_reads.selector == 'true' |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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15 @PREPROCESS_INPUT_FILES_ADDITIONAL@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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16 #end if |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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17 @PREPROCESS_NANOPORE_PACBIO_FILES@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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18 @PREPROCESS_SANGER_FILES@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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19 @PREPROCESS_CONTIGS_FILES@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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20 @PREPROCESS_ASSEMBLY_GRAPH_FILES@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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21 |
6
4a01e0d2892c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
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22 @OMP_THREADS@ |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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23 ## run |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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24 spades.py --meta --plasmid |
7
e5a3b75a271f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
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25 $operation_mode |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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26 -o 'output' |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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27 @RESOURCES@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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28 @INPUT_READS_MAIN@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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29 #if $additional_reads.selector == 'true' |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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30 @INPUT_READS_ADDITIONAL@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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31 #end if |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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32 ## reads |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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33 @NANOPORE_PACBIO@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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34 @SANGER@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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35 @CONTIGS@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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36 @ASSEMBLY_GRAPH@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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37 ## parameter |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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38 @KMER@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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39 @PHREDOFFSET@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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40 @PIPELINE_OPTIONS@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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41 ## postprocessing |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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42 @STATS@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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43 @CORRECTED@ |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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44 ]]></command> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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45 <inputs> |
7
e5a3b75a271f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
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46 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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47 <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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48 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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49 <section name="arf" title="Additional read files"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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50 <expand macro="nanopore_pacbio"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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51 <expand macro="sanger"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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52 <expand macro="contigs"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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53 <expand macro="assembly_graph"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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54 </section> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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55 <expand macro="kmer"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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56 <expand macro="phred"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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57 <expand macro="pipeline_options"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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58 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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59 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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60 </expand> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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61 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run."> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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62 <option value="cn" selected="true">Contigs</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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63 <option value="cs">Contigs stats</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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64 <option value="cr">Corrected reads</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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65 <option value="sc" selected="true">Scaffolds</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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66 <option value="ss">Scaffolds stats</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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67 <option value="l">Log</option> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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68 </param> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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69 </inputs> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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70 <outputs> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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71 <expand macro="out_cn"/> |
32ab23671cc1
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72 <expand macro="out_cr"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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73 <expand macro="out_cs"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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74 <expand macro="out_l"/> |
32ab23671cc1
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75 <expand macro="out_sc"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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76 <expand macro="out_ss"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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77 </outputs> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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78 <tests> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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79 <!-- |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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80 used in a test: |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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81 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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82 k, phred-offset, disablerr, iontorrent, only-assembler, only-error-correction |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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83 --> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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84 |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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85 <!-- #1 single, separate, fastq.gz, default parameters --> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
86 <test expect_num_outputs="2"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
87 <conditional name="singlePaired"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
88 <param name="sPaired" value="paired"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
89 <param name="input1" value="pl1.fq.gz"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
90 <param name="input2" value="pl2.fq.gz"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
91 </conditional> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
92 <output name="out_cn"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
93 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
94 <has_n_lines n="163"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
95 <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
96 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
97 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
98 <output name="out_sc"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
99 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
100 <has_n_lines n="163"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
101 <has_text_matching expression=">NODE\_1\_length\_9689.+"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
102 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
103 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
104 </test> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
105 <!-- #2 single, separate, fastq, custom parameters --> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
106 <test expect_num_outputs="6"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
107 <conditional name="singlePaired"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
108 <param name="sPaired" value="paired"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
109 <param name="input1" value="pl1.fq.gz"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
110 <param name="input2" value="pl2.fq.gz"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
111 </conditional> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
112 <conditional name="kmer_cond"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
113 <param name="kmer_sel" value="manual"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
114 <param name="manual" value="33"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
115 </conditional> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
116 <param name="phred_offset" value="33"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
117 <param name="optional_output" value="cn,cs,cr,sc,ss,l"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
118 <output name="out_cn"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
119 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
120 <has_n_lines n="162"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
121 <has_text_matching expression=">NODE\_1\_length\_9645\_cov\_.+"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
122 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
123 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
124 <output name="out_cs"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
125 <assert_contents> |
5
21da31ed41a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents:
0
diff
changeset
|
126 <has_n_lines n="2"/> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
127 <has_text_matching expression="#name	length	coverage"/> |
5
21da31ed41a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents:
0
diff
changeset
|
128 <has_text_matching expression="NODE_1	9645	13.774865_cutoff_0_type_circular"/> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
129 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
130 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
131 <output_collection name="out_cr" type="list" count="3"> |
7
e5a3b75a271f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents:
6
diff
changeset
|
132 <element name="pl1.fq.gz.fastq.00.0_0"> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
133 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
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|
134 <has_size value="71752" delta="1000"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
135 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
136 </element> |
7
e5a3b75a271f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents:
6
diff
changeset
|
137 <element name="pl2.fq.gz.fastq.00.0_0"> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
138 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
139 <has_size value="71752" delta="1000"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
140 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
141 </element> |
7
e5a3b75a271f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents:
6
diff
changeset
|
142 <element name="pl_unpaired.00.0_0"> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
143 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
144 <has_size value="423" delta="100"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
145 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
146 </element> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
147 </output_collection> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
148 <output name="out_sc"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
149 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
150 <has_n_lines n="162"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
151 <has_text_matching expression=">NODE\_1\_length\_9645\_cov\_.+"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
152 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
153 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
154 <output name="out_ss"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
155 <assert_contents> |
5
21da31ed41a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents:
0
diff
changeset
|
156 <has_n_lines n="2"/> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
157 <has_text_matching expression="#name	length	coverage"/> |
5
21da31ed41a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents:
0
diff
changeset
|
158 <has_text_matching expression="NODE_1	9645	13.774865_cutoff_0_type_circula"/> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
159 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
160 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
161 <output name="out_l"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
162 <assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
163 <has_text_matching expression="Thank you for using SPAdes!"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
164 </assert_contents> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
165 </output> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
166 </test> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
167 <!-- #3 --> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
168 <test expect_num_outputs="1"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
169 <conditional name="singlePaired"> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
170 <param name="sPaired" value="paired"/> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff
changeset
|
171 <param name="input1" value="pl1.fq.gz"/> |
32ab23671cc1
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172 <param name="input2" value="pl2.fq.gz"/> |
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173 </conditional> |
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174 <param name="operation_mode" value="--only-assembler"/> |
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175 <param name="optional_output" value="l"/> |
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176 <output name="out_l"> |
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177 <assert_contents> |
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178 <has_text_matching expression="Thank you for using SPAdes!"/> |
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179 </assert_contents> |
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180 </output> |
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181 </test> |
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182 <!-- #4, only corrected reads are created as an output --> |
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183 <test expect_num_outputs="2"> |
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184 <conditional name="singlePaired"> |
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185 <param name="sPaired" value="paired"/> |
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186 <param name="input1" value="pl1.fq.gz"/> |
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187 <param name="input2" value="pl2.fq.gz"/> |
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188 </conditional> |
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189 <param name="operation_mode" value="--only-error-correction"/> |
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190 <param name="optional_output" value="cr,l"/> |
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191 <output_collection name="out_cr" type="list" count="3"> |
7
e5a3b75a271f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
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192 <element name="pl1.fq.gz.fastq.00.0_0"> |
0
32ab23671cc1
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193 <assert_contents> |
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194 <has_size value="71752" delta="1000"/> |
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195 </assert_contents> |
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196 </element> |
7
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197 <element name="pl2.fq.gz.fastq.00.0_0"> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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198 <assert_contents> |
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199 <has_size value="71752" delta="1000"/> |
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200 </assert_contents> |
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201 </element> |
7
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202 <element name="pl_unpaired.00.0_0"> |
0
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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203 <assert_contents> |
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204 <has_size value="423" delta="100"/> |
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205 </assert_contents> |
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206 </element> |
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207 </output_collection> |
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208 <output name="out_l"> |
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209 <assert_contents> |
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210 <has_text_matching expression="Thank you for using SPAdes!"/> |
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211 </assert_contents> |
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212 </output> |
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213 </test> |
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214 </tests> |
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215 <help><![CDATA[ |
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216 .. class:: infomark |
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217 |
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218 **What it does** |
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219 |
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220 @HELP_WID@ |
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221 |
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222 metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data sets. |
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223 |
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224 **Input** |
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225 |
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226 @HELP_IN@ |
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227 |
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228 **Output** |
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229 |
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230 @HELP_OUT_C@ |
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231 @HELP_OUT_CS@ |
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232 @HELP_OUT_CR@ |
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233 @HELP_OUT_L@ |
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234 @HELP_OUT_S@ |
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235 @HELP_OUT_SS@ |
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236 |
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237 **References** |
32ab23671cc1
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238 |
6
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239 More information can be found on `github <https://github.com/ablab/spades>`_. |
0
32ab23671cc1
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240 ]]></help> |
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241 <expand macro="citations"> |
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242 <citation type="doi">10.1101/gr.241299.118</citation> |
32ab23671cc1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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243 </expand> |
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244 </tool> |