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annotate spades.xml @ 22:33368fec3b70 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
author iuc
date Tue, 23 Aug 2022 07:58:51 +0000
parents a789e163a670
children a90db5dbaaf3
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1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1" profile="20.01">
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2 <description>genome assembler for genomes of regular and single-cell projects</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <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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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 @OMP_THREADS@
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22 ## run
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23 spades.py
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24 $operation_mode
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25 -o 'output'
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26 @RESOURCES@
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27 @INPUT_READS_MAIN@
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28 #if $additional_reads.selector == 'true'
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29 @INPUT_READS_ADDITIONAL@
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30 #end if
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31 ## additional reads
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32 @NANOPORE_PACBIO@
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33 @SANGER@
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34 @CONTIGS@
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35 ## parameter
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36 #if $cov_cond.cov_cutoff == 'value':
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37 --cov-cutoff $cov_cond.manual
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38 #else:
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39 --cov-cutoff $cov_cond.cov_cutoff
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40 #end if
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41 @KMER@
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42 @PIPELINE_OPTIONS@
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43 @PHREDOFFSET@
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44
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45 ## postprocessing
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46 @STATS@
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47 @CORRECTED@
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48 ]]></command>
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49 <inputs>
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50 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
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51 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/>
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52 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/>
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53 <section name="arf" title="Additional read files">
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54 <expand macro="nanopore_pacbio"/>
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55 <expand macro="sanger"/>
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56 <expand macro="contigs"/>
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57 </section>
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58 <expand macro="pipeline_options">
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59 <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
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60 <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
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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 <expand macro="covcutoff"/>
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65 <expand macro="kmer" help="If --sc is set the default values are 21,33,55. For multicell datasets K values are automatically selected using maximum read length."/>
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66 <expand macro="phred"/>
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67 <expand macro="optional_output"/>
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68 </inputs>
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69 <outputs>
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70 <expand macro="out_ag"/>
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71 <expand macro="out_ags"/>
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72 <expand macro="out_cn"/>
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73 <expand macro="out_cp"/>
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74 <expand macro="out_cr"/>
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75 <expand macro="out_cs"/>
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76 <expand macro="out_l"/>
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77 <expand macro="out_sc"/>
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78 <expand macro="out_sp"/>
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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 single library: 12, 1, 2
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85 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
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86 k, phred-offset, disablerr, iontorrent, careful, isolate, only-assembler, only-error-correction, sc
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87
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88 not used in a test:
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89 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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parents: 13
diff changeset
90 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
91
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
92 <!-- #1 single, interlaced, fastq.gz, default parameters -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
93 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
94 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
95 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
96 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
97 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
98 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
99 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
100 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
101 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
102 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
103 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
104 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
105 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
106 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
107 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
108 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
109 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
110 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
111 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
112 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
113 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
114 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
115 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
116 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
117 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
118 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
119 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
120 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
121 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
122 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
123 <!-- #2 single, separate, fastq, custom parameters -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
124 <test expect_num_outputs="9">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
125 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
126 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
127 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
128 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
129 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
130 <param name="mode_sel" value="--isolate,--disable-rr,--iontorrent"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
131 <conditional name="cov_cond">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
132 <param name="cov_cutoff" value="auto"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
133 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
134 <conditional name="kmer_cond">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
135 <param name="kmer_sel" value="manual"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
136 <param name="manual" value="33"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
137 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
138 <param name="phred_offset" value="33"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
139 <param name="optional_output" value="ag,ags,cn,cp,cs,sc,sp,ss,l"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
140 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
141 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
142 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
143 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
144 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
145 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
146 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
147 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
148 <has_n_lines n="1"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
149 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
150 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
151 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
152 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
153 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
154 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
155 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
156 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
157 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
158 <output name="out_cp">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
159 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
160 <has_n_lines n="0"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
161 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
162 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
163 <output name="out_cs">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
164 <assert_contents>
20
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
165 <has_n_lines n="2"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
166 <has_text_matching expression="#name&#009;length&#009;coverage"/>
20
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
167 <has_text_matching expression="NODE_1&#009;1000&#009;225.723888"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
168 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
169 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
170 <output name="out_l">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
171 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
172 <has_text_matching expression="Thank you for using SPAdes!"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
173 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
174 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
175 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
176 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
177 <has_n_lines n="0"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
178 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
179 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
180 <output name="out_sp">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
181 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
182 <has_n_lines n="0"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
183 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
184 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
185 <output name="out_ss">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
186 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
187 <has_n_lines n="0"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
188 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
189 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
190 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
191 <!-- #3 single, separate, fasta, default parameters -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
192 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
193 <param name="operation_mode" value="--only-assembler"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
194 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
195 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
196 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
197 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
198 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
199 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
200 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
201 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
202 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
203 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
204 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
205 <output name="out_ags">
6
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340
iuc
parents: 5
diff changeset
206 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
207 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
208 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
209 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
210 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
211 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
212 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
213 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
214 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
215 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
216 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
217 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
218 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
219 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
220 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
221 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
222 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
223 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
224 <!-- #4 multiple, single & paired-end within same library: careful mode -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
225 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
226 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
227 <param name="sPaired" value="single"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
228 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
229 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
230 <conditional name="additional_reads">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
231 <param name="selector" value="true"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
232 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
233 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
234 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
235 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
236 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
237 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
238 <param name="mode_sel" value="--careful"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
239 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
240 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
241 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
242 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
243 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
244 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
245 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
246 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
247 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
248 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
249 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
250 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
251 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
252 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
253 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
254 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
255 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
256 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
257 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
258 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
259 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
260 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
261 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
262 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
263 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
264 <!-- #5 multiple, single & paired-end in different libraries -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
265 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
266 <param name="operation_mode" value="--only-assembler"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
267 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
268 <param name="sPaired" value="single"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
269 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
270 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
271 <conditional name="additional_reads">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
272 <param name="selector" value="true"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
273 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
274 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
275 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
276 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
277 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
278 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
279 <param name="mode_sel" value="--careful"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
280 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
281 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
282 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
283 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
284 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
285 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
286 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
287 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
288 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
289 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
290 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
291 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
292 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
293 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
294 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
295 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
296 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
297 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
298 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
299 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
300 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
301 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
302 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
303 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
304 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
305 <!-- #6 only corrected reads are created as an output -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
306 <test expect_num_outputs="2">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
307 <param name="operation_mode" value="--only-error-correction"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
308 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
309 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
310 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
311 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
312 <param name="mode_sel" value="--careful"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
313 <param name="optional_output" value="cr,l"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
314 <output_collection name="out_cr" type="list" count="3">
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
315 <element name="ecoli_1K.fastq.gz_1.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
316 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
317 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
318 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
319 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
320 <element name="ecoli_1K.fastq.gz_2.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
321 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
322 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
323 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
324 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
325 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
326 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
327 <has_size value="20" delta="5"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
328 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
329 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
330 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
331 <output name="out_l">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
332 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
333 <has_text_matching expression="Thank you for using SPAdes!"/>
6
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340
iuc
parents: 5
diff changeset
334 </assert_contents>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340
iuc
parents: 5
diff changeset
335 </output>
5
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 4
diff changeset
336 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
337 <!-- #7 only corrected reads are created as an output -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
338 <test expect_num_outputs="2">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
339 <param name="operation_mode" value="--only-error-correction"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
340 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
341 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
342 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
343 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
344 <param name="mode_sel" value="--careful,--sc"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
345 <param name="optional_output" value="cr,l"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
346 <output_collection name="out_cr" type="list" count="3">
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
347 <element name="ecoli_1K.fastq.gz_1.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
348 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
349 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
350 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
351 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
352 <element name="ecoli_1K.fastq.gz_2.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
353 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
354 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
355 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
356 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
357 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
358 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
359 <has_size value="20" delta="5"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
360 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
361 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
362 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
363 <output name="out_l">
9
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
364 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
365 <has_text_matching expression="Thank you for using SPAdes!"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
366 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
367 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
368 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
369 <!-- #8 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
370 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
371 <param name="operation_mode" value="--only-assembler"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
372 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
373 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
374 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
375 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
376 <param name="mode_sel" value="--sc"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
377 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
378 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
379 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
380 <has_text_matching expression=">EDGE_7_length_1000_cov_140.639153"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
381 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
382 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
383 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
384 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
385 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
386 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
387 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
388 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
389 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
390 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
391 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
392 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
393 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
394 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
395 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
396 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
397 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
398 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
9
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
399 </assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
400 </output>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
401 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
402 <!-- #9 only corrected reads are created as an output -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
403 <test expect_num_outputs="2">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
404 <param name="operation_mode" value="--only-error-correction"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
405 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
406 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
407 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
408 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
409 <param name="optional_output" value="cr,l"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
410 <output_collection name="out_cr" type="list" count="3">
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
411 <element name="ecoli_1K.fastq.gz_1.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
412 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
413 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
414 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
415 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
416 <element name="ecoli_1K.fastq.gz_2.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
417 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
418 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
419 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
420 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
421 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
422 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
423 <has_size value="20" delta="5"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
424 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
425 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
426 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
427 <output name="out_l">
9
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
428 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
429 <has_text_matching expression="Thank you for using SPAdes!"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
430 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
431 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
432 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
433 <!-- #10 only corrected reads are created as an output -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
434 <test expect_num_outputs="2">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
435 <param name="operation_mode" value="--only-error-correction"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
436 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
437 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
438 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
439 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
440 <param name="mode_sel" value="--sc"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
441 <param name="optional_output" value="cr,l"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
442 <output_collection name="out_cr" type="list" count="3">
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
443 <element name="ecoli_1K.fastq.gz_1.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
444 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
445 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
446 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
447 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
448 <element name="ecoli_1K.fastq.gz_2.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
449 <assert_contents>
16
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents: 14
diff changeset
450 <has_size value="130317" delta="5000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
451 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
452 </element>
22
33368fec3b70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 21
diff changeset
453 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
454 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
455 <has_size value="20" delta="5"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
456 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
457 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
458 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
459 <output name="out_l">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
460 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
461 <has_text_matching expression="Thank you for using SPAdes!"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
462 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
463 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
464 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
465 <!-- #11 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
466 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
467 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
468 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
469 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
470 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
471 <param name="mode_sel" value="--sc"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
472 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
473 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
474 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
475 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
476 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
477 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
478 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
479 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
480 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
481 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
482 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
483 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
484 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
485 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
486 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
487 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
488 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
489 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
490 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
491 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
492 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
493 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
9
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
494 </assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
495 </output>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
496 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
497 <!-- #12 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
498 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
499 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
500 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
501 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
502 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
503 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
504 <param name="mode_sel" value="--sc,--careful"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
505 <output name="out_ag">
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
506 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
507 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
508 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
509 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
510 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
511 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
512 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
513 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
514 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
515 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
516 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
517 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
518 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
519 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
520 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
521 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
522 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
523 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
524 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
525 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
526 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
527 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
528 </output>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
529 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
530 <!-- #13 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
531 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
532 <param name="operation_mode" value="--only-assembler"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
533 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
534 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
535 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
536 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
537 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
538 <param name="mode_sel" value="--sc,--careful"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
539 <output name="out_ag">
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
540 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
541 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
542 <has_text_matching expression=">EDGE\_.+"/>
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
543 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
544 </output>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
545 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
546 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
547 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
548 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
549 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
550 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
551 <output name="out_cn">
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
552 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
553 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
554 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
555 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
556 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
557 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
558 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
559 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
560 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
561 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
562 </output>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
563 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
564 <!-- #14 interlaced, fastq.gz, hybrid assembly: nanopore, pacbio sanger and trustedcontigs -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
565 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
566 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
567 <param name="sPaired" value="paired_interlaced"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
568 <param name="input1" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
569 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
570 <section name="arf">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
571 <param name="nanopore" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
572 <param name="pacbio" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
573 <param name="sanger" value="ecoli_1K.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
574 <param name="trusted_contigs" value="ecoli_1K.fasta.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
575 </section>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
576 <assert_command>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
577 <has_text text="--nanopore"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
578 <has_text text="--pacbio"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
579 <has_text text="--sanger"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
580 <has_text text="--trusted-contigs"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
581 </assert_command>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
582 <output name="out_ag">
10
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
583 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
584 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
585 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
586 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
587 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
588 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
589 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
590 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
591 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
592 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
593 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
594 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
595 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
596 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
597 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
598 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
599 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
600 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
601 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
602 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
603 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
10
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
604 </assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
605 </output>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
606 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
607 <!-- #15 mate-pair reads orientation rf-->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
608 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
609 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
610 <param name="sPaired" value="paired"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
611 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
612 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
613 <param name="type_paired" value="hqmp"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
614 <param name="orientation" value="rf"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
615 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
616 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
617 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
618 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
619 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
620 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
621 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
622 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
623 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
624 <has_n_lines n="1"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
625 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
626 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
627 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
628 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
629 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
630 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
631 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
632 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
633 <output name="out_sc">
10
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
634 <assert_contents>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
635 <has_n_lines n="0"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
636 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
637 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
638 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
639 <!-- #16 high-quality mate-pair reads collection-->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
640 <test expect_num_outputs="4">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
641 <conditional name="singlePaired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
642 <param name="sPaired" value="paired_collection"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
643 <param name="input">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
644 <collection type="list:paired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
645 <element name="ecoli.fastq">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
646 <collection type="paired">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
647 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
648 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
649 </collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
650 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
651 </collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
652 </param>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
653 <param name="type_paired" value="hqmp"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
654 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
655 <output name="out_ag">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
656 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
657 <has_n_lines n="36"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
658 <has_text_matching expression=">EDGE_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
659 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
660 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
661 <output name="out_ags">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
662 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
663 <has_n_lines n="2"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
664 <has_text_matching expression="S.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
665 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
666 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
667 <output name="out_cn">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
668 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
669 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
670 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
671 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
672 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
673 <output name="out_sc">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
674 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
675 <has_n_lines n="18"/>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
676 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
10
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
677 </assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
678 </output>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
679 </test>
20
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
680 <!-- #17 Fix stats script -->
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
681 <test expect_num_outputs="1">
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
682 <conditional name="singlePaired">
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
683 <param name="sPaired" value="single"/>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
684 <param name="input1" value="ecoli_1K.fastq.gz"/>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
685 </conditional>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
686 <param name="optional_output" value="ss"/>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
687 <output name="out_ss">
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
688 <assert_contents>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
689 <has_n_lines n="2"/>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
690 <has_text text="NODE_1&#009;1000&#009;140.620106"/>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
691 <has_text_matching expression="#name&#009;length&#009;coverage"/>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
692 </assert_contents>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
693 </output>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
694 </test>
5
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 4
diff changeset
695 </tests>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
696 <help><![CDATA[
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
697 .. class:: infomark
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
698
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
699 **What it does**
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
700
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
701 @HELP_WID@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
702
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
703 **Input**
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
704
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
705 @HELP_IN@
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
706
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
707 **Output**
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
708
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
709 @HELP_OUT_AG@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
710 @HELP_OUT_AGS@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
711 @HELP_OUT_C@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
712 @HELP_OUT_CP@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
713 @HELP_OUT_CR@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
714 @HELP_OUT_CS@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
715 @HELP_OUT_L@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
716 @HELP_OUT_S@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
717 @HELP_OUT_SP@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
718 @HELP_OUT_SS@
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
719
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
720
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
721 -------------------
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
722
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
723 .. class:: infomark
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
724
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
725 **IonTorrent data**
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
726
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
727 @IONTORRENT@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
728
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
729 -------------------
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
730
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
731 .. class:: infomark
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
732
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
733 **References**
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
734
21
a789e163a670 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 20
diff changeset
735 More information are available on `github <https://github.com/ablab/spades>`_.
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
736 ]]></help>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
737 <expand macro="citations">
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
738 <citation type="doi">10.1089/cmb.2012.0021</citation>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
739 <citation type="doi">10.1007/978-3-642-37195-0_13</citation>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
740 </expand>
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
741 </tool>