Mercurial > repos > estrain > spades_cpu7mem28

annotate spades_cpu7mem28.xml @ 1:45b5f747c900 draft default tip

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planemo upload commit 611f051119d03ed04af67a33e403496bc3e7cc1e
author galaxytrakr
date Thu, 19 Mar 2026 15:43:04 +0000
parents f69397b32f52
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1 <tool id="spades_cpu7mem28" name="SPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>genome assembler for genomes of regular and single-cell projects</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">spades</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <expand macro="version_command"/>
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12 <command detect_errors="exit_code"><![CDATA[
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13
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14 #set $library = 1
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15
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16 @PREPROCESS_INPUT_FILES_MAIN@
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17 #if $additional_reads.selector == 'true'
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18 @PREPROCESS_INPUT_FILES_ADDITIONAL@
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19 #end if
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20 @PREPROCESS_NANOPORE_PACBIO_FILES@
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21 @PREPROCESS_CONTIGS_FILES@
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22 @PREPROCESS_SANGER_FILES@
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23
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24 @OMP_THREADS@
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25 ## run
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26 spades.py
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27 $operation_mode
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28 -o 'output'
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29 @RESOURCES@
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30 @INPUT_READS_MAIN@
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31 #if $additional_reads.selector == 'true'
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32 @INPUT_READS_ADDITIONAL@
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33 #end if
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34 ## additional reads
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35 @NANOPORE_PACBIO@
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36 @SANGER@
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37 @CONTIGS@
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38 ## parameter
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39 #if $cov_cond.cov_cutoff == 'value':
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40 --cov-cutoff $cov_cond.manual
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41 #else:
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42 --cov-cutoff $cov_cond.cov_cutoff
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43 #end if
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44 @KMER@
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45 @PIPELINE_OPTIONS@
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46 @PHREDOFFSET@
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47
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48 ## postprocessing
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49 @STATS@
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50 ]]></command>
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51 <inputs>
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52 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
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53 <expand macro="input_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
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54 <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
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55 <section name="arf" title="Additional read files">
1
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56
0
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57 <expand macro="nanopore_pacbio"/>
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58 <expand macro="sanger"/>
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59 <expand macro="contigs"/>
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60 </section>
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61 <expand macro="pipeline_options" additional_help="&quot;Isolate&quot; is not compatible with &quot;Careful&quot; and Operation mode &quot;Only error correction&quot;">
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62 <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
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63 <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
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64 <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
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65 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
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66 </expand>
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67 <expand macro="covcutoff"/>
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68 <expand macro="kmer" help="If --sc is set the default values are 21,33,55. For multicell datasets K values are automatically selected using maximum read length."/>
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69 <expand macro="phred"/>
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70 <expand macro="optional_output"/>
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71 </inputs>
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72 <outputs>
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73 <expand macro="out_ag"/>
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74 <expand macro="out_ags"/>
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75 <expand macro="out_cn"/>
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76 <expand macro="out_cp"/>
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77 <expand macro="out_cr"/>
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78 <expand macro="out_cs"/>
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79 <expand macro="out_l"/>
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80 <expand macro="out_sc"/>
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81 <expand macro="out_sp"/>
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82 <expand macro="out_ss"/>
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83 </outputs>
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84 <!-- tests/help/citations unchanged -->
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85 </tool>
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86