Mercurial > repos > iuc > spades_rnaviralspades

annotate rnaviralspades.xml @ 1:11d7955eddf9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
author iuc
date Mon, 24 Jan 2022 18:44:03 +0000
parents 5df83f4bad67
children 249f6a28c751
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1 <tool id="spades_rnaviralspades" name="rnaviralSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>de novo assembler for transcriptomes, metatranscriptomes and metaviromes</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 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10
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11 #set $library = 1
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12
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13 @PREPROCESS_INPUT_FILES_MAIN@
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14 #if $additional_reads.selector == 'true'
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15 @PREPROCESS_INPUT_FILES_ADDITIONAL@
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16 #end if
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17 @PREPROCESS_NANOPORE_PACBIO_FILES@
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18 @PREPROCESS_CONTIGS_FILES@
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19 @PREPROCESS_SANGER_FILES@
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20
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21 ## run
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22 spades.py --rnaviral
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23 -o 'output'
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24 @RESOURCES@
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25 @INPUT_READS_MAIN@
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26 #if $additional_reads.selector == 'true'
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27 @INPUT_READS_ADDITIONAL@
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28 #end if
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29 ## additional reads
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30 @NANOPORE_PACBIO@
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31 @SANGER@
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32 @CONTIGS@
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33 ## parameter
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34 @KMER@
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35 @PIPELINE_OPTIONS@
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36 @PHREDOFFSET@
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37
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38 ## postprocessing
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39 @STATS@
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40 @CORRECTED@
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41 ]]></command>
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42 <inputs>
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43 <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/>
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44 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
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45 <section name="arf" title="Additional read files">
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46 <expand macro="sanger"/>
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47 <expand macro="nanopore_pacbio"/>
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48 <expand macro="contigs"/>
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49 </section>
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50 <expand macro="pipeline_options">
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51 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
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52 </expand>
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53 <expand macro="kmer" help="By default rnaSPAdes uses 2 k-mer sizes, which are automatically detected using read length (approximately one third and half of the maximal read length). We recommend not to change this parameter because smaller k-mer sizes typically result in multiple chimeric (misassembled) transcripts."/>
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54 <expand macro="phred"/>
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55 <expand macro="optional_output"/>
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56 </inputs>
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57 <outputs>
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58 <expand macro="out_ag"/>
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59 <expand macro="out_ags"/>
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60 <expand macro="out_cn"/>
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61 <expand macro="out_cp"/>
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62 <expand macro="out_cr"/>
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63 <expand macro="out_cs"/>
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64 <expand macro="out_l"/>
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65 <expand macro="out_sc"/>
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66 <expand macro="out_sp"/>
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67 <expand macro="out_ss"/>
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68 </outputs>
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69 <tests>
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70 <!--
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71 used in a test:
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72 single library: 12, 1, 2
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73 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
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74 k, phred-offset, disablerr, iontorrent, careful, isolate, only-assembler, only-error-correction, sc
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75
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76 not used in a test:
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77 single library: merged, s
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78 multiple libraries: pe#-m, pe#-s, mp#-12, mp#-1, mp#-2, mp#-<or>, mp#-s, hqmp#-12, hqmp#-1, hqmp#-2, hqmp#-s, hqmp#-<or>, nxmate#-1, nxmate-#2
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79 pacbio, nanopore, sanger, trusted-contigs, untrusted-contigs, tslr
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80 -->
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81
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82 <!-- #1 single, interlaced, fastq.gz, default parameters -->
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83 <test expect_num_outputs="4">
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84 <conditional name="singlePaired">
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85 <param name="sPaired" value="paired_interlaced"/>
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86 <param name="input1" value="ecoli_1K.fastq.gz"/>
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87 </conditional>
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88 <output name="out_ag">
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89 <assert_contents>
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90 <has_n_lines n="36"/>
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diff changeset
91 <has_text_matching expression=">EDGE\_3\_length.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
92 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
93 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
94 <output name="out_ags">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
95 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
96 <has_n_lines n="2"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
97 <has_text_matching expression="S.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
98 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
99 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
100 <output name="out_cn">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
101 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
102 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
103 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
104 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
105 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
106 <output name="out_sc">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
107 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
108 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
109 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
110 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
111 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
112 </test>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
113 <!-- #2 single, separate, fastq, all outputs -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
114 <test expect_num_outputs="10">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
115 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
116 <param name="sPaired" value="paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
117 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
118 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
119 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
120 <conditional name="cov_cond">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
121 <param name="cov_cutoff" value="auto"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
122 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
123 <param name="mode_sel" value="--disable-rr,--iontorrent"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
124 <param name="phred_offset" value="33"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
125 <param name="optional_output" value="ag,ags,cn,cp,cs,cr,sc,sp,ss,l"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
126 <output name="out_ag">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
127 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
128 <has_n_lines n="36"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
129 <has_text_matching expression=">EDGE.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
130 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
131 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
132 <output name="out_ags">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
133 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
134 <has_n_lines n="1"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
135 <has_text_matching expression="S.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
136 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
137 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
138 <output name="out_cn">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
139 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
140 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
141 <has_text_matching expression=">NODE.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
142 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
143 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
144 <output name="out_cp">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
145 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
146 <has_n_lines n="0"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
147 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
148 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
149 <output_collection name="out_cr" type="list" count="2">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
150 <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
151 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
152 <has_size value="34468" delta="1000"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
153 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
154 </element>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
155 <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
156 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
157 <has_size value="34468" delta="1000"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
158 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
159 </element>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
160 </output_collection>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
161 <output name="out_cs">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
162 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
163 <has_n_lines n="1"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
164 <has_text_matching expression="#name&#009;length&#009;coverage"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
165 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
166 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
167 <output name="out_l">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
168 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
169 <has_text_matching expression="Thank you for using SPAdes!"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
170 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
171 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
172 <output name="out_sc">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
173 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
174 <has_n_lines n="0"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
175 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
176 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
177 <output name="out_sp">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
178 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
179 <has_n_lines n="0"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
180 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
181 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
182 <output name="out_ss">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
183 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
184 <has_n_lines n="0"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
185 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
186 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
187 </test>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
188 <!-- #3 single, separate, fasta, default parameters -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
189 <test expect_num_outputs="4">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
190 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
191 <param name="sPaired" value="paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
192 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
193 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
194 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
195 <output name="out_ag">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
196 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
197 <has_n_lines n="36"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
198 <has_text_matching expression=">EDGE_3_length_1000_cov_163.370137"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
199 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
200 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
201 <output name="out_ags">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
202 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
203 <has_n_lines n="2"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
204 <has_text_matching expression="S.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
205 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
206 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
207 <output name="out_cn">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
208 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
209 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
210 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
211 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
212 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
213 <output name="out_sc">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
214 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
215 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
216 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
217 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
218 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
219 </test>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
220 <!-- #4 multiple, single & paired-end-->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
221 <test expect_num_outputs="4">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
222 <param name="operation_mode" value="--only-assembler"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
223 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
224 <param name="sPaired" value="single"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
225 <param name="input1" value="ecoli_1K.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
226 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
227 <conditional name="additional_reads">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
228 <param name="selector" value="true"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
229 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
230 <param name="sPaired" value="paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
231 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
232 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
233 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
234 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
235 <section name="arf">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
236 <param name="nanopore" value="ecoli_1K.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
237 <param name="pacbio" value="ecoli_1K.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
238 <param name="sanger" value="ecoli_1K.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
239 <param name="trusted_contigs" value="ecoli_1K.fasta.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
240 </section>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
241 <assert_command>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
242 <has_text text="--nanopore"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
243 <has_text text="--pacbio"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
244 <has_text text="--sanger"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
245 <has_text text="--trusted-contigs"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
246 </assert_command>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
247 <output name="out_ag">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
248 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
249 <has_n_lines n="36"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
250 <has_text_matching expression=">EDGE_.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
251 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
252 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
253 <output name="out_ags">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
254 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
255 <has_n_lines n="2"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
256 <has_text_matching expression="S.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
257 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
258 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
259 <output name="out_cn">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
260 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
261 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
262 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
263 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
264 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
265 <output name="out_sc">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
266 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
267 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
268 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
269 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
270 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
271 </test>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
272 <!-- #5 Multiple samples, different libraries: hybrid assembly: nanopore, pacbio -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
273 <test expect_num_outputs="4">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
274 <param name="operation_mode" value="--only-assembler"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
275 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
276 <param name="sPaired" value="single"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
277 <param name="input1" value="ecoli_1K.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
278 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
279 <conditional name="additional_reads">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
280 <param name="selector" value="true"/>
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iuc
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281 <conditional name="singlePaired">
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iuc
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282 <param name="sPaired" value="paired"/>
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283 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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284 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
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iuc
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285 </conditional>
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iuc
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286 <param name="library_number" value="false"/>
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iuc
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287 </conditional>
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288
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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289 <output name="out_ag">
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iuc
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290 <assert_contents>
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iuc
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291 <has_n_lines n="36"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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292 <has_text_matching expression=">EDGE_3_length_1000_cov_326.740273"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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293 </assert_contents>
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iuc
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294 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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295 <output name="out_ags">
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iuc
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296 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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297 <has_n_lines n="2"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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298 <has_text_matching expression="S.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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299 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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diff changeset
300 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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301 <output name="out_cn">
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iuc
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302 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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303 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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304 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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305 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
306 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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307 <output name="out_sc">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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308 <assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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309 <has_n_lines n="18"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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310 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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311 </assert_contents>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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312 </output>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
313 </test>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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314 </tests>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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315 <help><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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316 .. class:: infomark
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iuc
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317
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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318 **What it does**
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iuc
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319
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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320 @HELP_WID@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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321
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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322 rnaviralSPAdes is a pipeline specially designed for de novo assembler tailored for RNA viral datasets (transcriptome, metatranscriptome and metavirome).
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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323
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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324 **Input**
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iuc
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325
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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326 @HELP_IN@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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327
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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328 **Output**
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iuc
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329
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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330 @HELP_OUT_AG@
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iuc
parents:
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331 @HELP_OUT_AGS@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
332 @HELP_OUT_C@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
333 @HELP_OUT_CP@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
334 @HELP_OUT_CR@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
335 @HELP_OUT_CS@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
336 @HELP_OUT_L@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
337 @HELP_OUT_S@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
338 @HELP_OUT_SP@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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339 @HELP_OUT_SS@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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340
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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341
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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342 -------------------
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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343
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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344 .. class:: infomark
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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345
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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346 **IonTorrent data**
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iuc
parents:
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347
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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348 @IONTORRENT@
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iuc
parents:
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349
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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350 -------------------
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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351
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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352 .. class:: infomark
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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353
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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354 **References**
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iuc
parents:
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355
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
356 More information are available on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
357 ]]></help>
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parents:
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358 <expand macro="citations"/>
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iuc
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359 </tool>