Mercurial > repos > iuc > spades_metaplasmidspades

annotate metaplasmidspades.xml @ 9:7e27faaad80e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f53f7f297e551bf58e753752edd0dae5205bbc77
author iuc
date Mon, 15 Apr 2024 19:39:12 +0000
parents 037f9927c4ff
children
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32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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1 <tool id="spades_metaplasmidspades" name="metaplasmidSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>extract and assembly plasmids from metagenomic data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
8
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6 <xrefs>
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7 <xref type="bio.tools">metaplasmidspades</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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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_SANGER_FILES@
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22 @PREPROCESS_CONTIGS_FILES@
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23 @PREPROCESS_ASSEMBLY_GRAPH_FILES@
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24
6
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25 @OMP_THREADS@
0
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26 ## run
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27 spades.py --meta --plasmid
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28 $operation_mode
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29 -o 'output'
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30 @RESOURCES@
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31 @INPUT_READS_MAIN@
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32 #if $additional_reads.selector == 'true'
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33 @INPUT_READS_ADDITIONAL@
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34 #end if
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35 ## reads
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36 @NANOPORE_PACBIO@
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37 @SANGER@
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38 @CONTIGS@
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39 @ASSEMBLY_GRAPH@
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40 ## parameter
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41 @KMER@
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42 @PHREDOFFSET@
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43 @PIPELINE_OPTIONS@
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44 ## postprocessing
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45 @STATS@
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46 @CORRECTED@
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47 ]]></command>
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48 <inputs>
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49 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
0
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50 <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
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51 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
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52 <section name="arf" title="Additional read files">
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53 <expand macro="nanopore_pacbio"/>
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54 <expand macro="sanger"/>
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55 <expand macro="contigs"/>
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56 <expand macro="assembly_graph"/>
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57 </section>
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58 <expand macro="kmer"/>
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59 <expand macro="phred"/>
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60 <expand macro="pipeline_options">
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61 <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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62 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
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63 </expand>
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64 <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.">
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65 <option value="cn" selected="true">Contigs</option>
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66 <option value="cs">Contigs stats</option>
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67 <option value="cr">Corrected reads</option>
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68 <option value="sc" selected="true">Scaffolds</option>
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69 <option value="ss">Scaffolds stats</option>
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70 <option value="l">Log</option>
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71 </param>
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72 </inputs>
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73 <outputs>
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74 <expand macro="out_cn"/>
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75 <expand macro="out_cr"/>
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76 <expand macro="out_cs"/>
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77 <expand macro="out_l"/>
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78 <expand macro="out_sc"/>
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79 <expand macro="out_ss"/>
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80 </outputs>
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81 <tests>
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82 <!--
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83 used in a test:
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84 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
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85 k, phred-offset, disablerr, iontorrent, only-assembler, only-error-correction
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86 -->
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87
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88 <!-- #1 single, separate, fastq.gz, default parameters -->
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89 <test expect_num_outputs="2">
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90 <conditional name="singlePaired">
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91 <param name="sPaired" value="paired"/>
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92 <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
93 <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
94 </conditional>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
95 <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
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 <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
98 <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
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 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
101 <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
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 <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
104 <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
105 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
106 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
107 </test>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
108 <!-- #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
109 <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
110 <conditional name="singlePaired">
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
111 <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
112 <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
113 <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
114 </conditional>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
115 <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
116 <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
117 <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
118 </conditional>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
119 <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
120 <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
121 <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
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 <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
124 <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
125 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
126 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
127 <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
128 <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
129 <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
130 <has_text_matching expression="#name&#009;length&#009;coverage"/>
5
21da31ed41a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 0
diff changeset
131 <has_text_matching expression="NODE_1&#009;9645&#009;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
132 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
133 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
134 <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
135 <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
136 <assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
137 <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
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 </element>
7
e5a3b75a271f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
140 <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
141 <assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
142 <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
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 </element>
7
e5a3b75a271f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
145 <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
146 <assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
147 <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
148 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
149 </element>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
150 </output_collection>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
151 <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
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 <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
154 <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
155 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
156 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
157 <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
158 <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
159 <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
160 <has_text_matching expression="#name&#009;length&#009;coverage"/>
5
21da31ed41a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 0
diff changeset
161 <has_text_matching expression="NODE_1&#009;9645&#009;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
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 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
164 <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
165 <assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
166 <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
167 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
168 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
169 </test>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
170 <!-- #3 -->
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
171 <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
172 <conditional name="singlePaired">
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
173 <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
174 <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
175 <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
176 </conditional>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
177 <param name="operation_mode" value="--only-assembler"/>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
178 <param name="optional_output" value="l"/>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
179 <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
180 <assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
181 <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
182 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
183 </output>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
184 </test>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
185 <!-- #4, only corrected reads are created as an output -->
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
186 <test expect_num_outputs="2">
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187 <conditional name="singlePaired">
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188 <param name="sPaired" value="paired"/>
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189 <param name="input1" value="pl1.fq.gz"/>
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190 <param name="input2" value="pl2.fq.gz"/>
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191 </conditional>
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192 <param name="operation_mode" value="--only-error-correction"/>
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193 <param name="optional_output" value="cr,l"/>
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194 <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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195 <element name="pl1.fq.gz.fastq.00.0_0">
0
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196 <assert_contents>
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197 <has_size value="71752" delta="1000"/>
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198 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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199 </element>
7
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200 <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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201 <assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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202 <has_size value="71752" delta="1000"/>
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203 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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204 </element>
7
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205 <element name="pl_unpaired.00.0_0">
0
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206 <assert_contents>
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207 <has_size value="423" delta="100"/>
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208 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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209 </element>
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210 </output_collection>
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211 <output name="out_l">
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212 <assert_contents>
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213 <has_text_matching expression="Thank you for using SPAdes!"/>
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214 </assert_contents>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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215 </output>
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216 </test>
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217 </tests>
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218 <help><![CDATA[
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219 .. class:: infomark
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220
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221 **What it does**
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222
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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223 @HELP_WID@
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224
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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225 metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data sets.
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226
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227 **Input**
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228
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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229 @HELP_IN@
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230
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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231 **Output**
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232
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233 @HELP_OUT_C@
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234 @HELP_OUT_CS@
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235 @HELP_OUT_CR@
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236 @HELP_OUT_L@
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237 @HELP_OUT_S@
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238 @HELP_OUT_SS@
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239
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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240 **References**
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241
6
4a01e0d2892c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
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242 More information can be found on `github <https://github.com/ablab/spades>`_.
0
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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243 ]]></help>
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244 <expand macro="citations">
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245 <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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246 </expand>
32ab23671cc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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247 </tool>