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annotate spades.xml @ 26:b512435320e3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
author iuc
date Wed, 12 Mar 2025 21:46:56 +0000
parents d5887ace0dd4
children
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1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>genome assembler for genomes of regular and single-cell projects</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">spades</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <expand macro="version_command"/>
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12 <command detect_errors="exit_code"><![CDATA[
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13
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14 #set $library = 1
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15
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16 @PREPROCESS_INPUT_FILES_MAIN@
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17 #if $additional_reads.selector == 'true'
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18 @PREPROCESS_INPUT_FILES_ADDITIONAL@
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19 #end if
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20 @PREPROCESS_NANOPORE_PACBIO_FILES@
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21 @PREPROCESS_CONTIGS_FILES@
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22 @PREPROCESS_SANGER_FILES@
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23
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24 @OMP_THREADS@
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25 ## run
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26 spades.py
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27 $operation_mode
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28 -o 'output'
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29 @RESOURCES@
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30 @INPUT_READS_MAIN@
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31 #if $additional_reads.selector == 'true'
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32 @INPUT_READS_ADDITIONAL@
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33 #end if
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34 ## additional reads
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35 @NANOPORE_PACBIO@
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36 @SANGER@
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37 @CONTIGS@
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38 ## parameter
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39 #if $cov_cond.cov_cutoff == 'value':
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40 --cov-cutoff $cov_cond.manual
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41 #else:
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42 --cov-cutoff $cov_cond.cov_cutoff
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43 #end if
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44 @KMER@
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45 @PIPELINE_OPTIONS@
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46 @PHREDOFFSET@
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47
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48 ## postprocessing
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49 @STATS@
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50 ]]></command>
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51 <inputs>
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52 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
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53 <expand macro="input_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
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54 <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
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55 <section name="arf" title="Additional read files">
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56 <expand macro="nanopore_pacbio"/>
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57 <expand macro="sanger"/>
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58 <expand macro="contigs"/>
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59 </section>
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60 <expand macro="pipeline_options" additional_help="&quot;Isolate&quot; is not compatible with &quot;Careful&quot; and Operation mode &quot;Only error correction&quot;">
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61 <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
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62 <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
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63 <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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64 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
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65 </expand>
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66 <expand macro="covcutoff"/>
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67 <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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68 <expand macro="phred"/>
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69 <expand macro="optional_output"/>
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70 </inputs>
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71 <outputs>
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72 <expand macro="out_ag"/>
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73 <expand macro="out_ags"/>
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74 <expand macro="out_cn"/>
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75 <expand macro="out_cp"/>
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76 <expand macro="out_cr"/>
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77 <expand macro="out_cs"/>
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78 <expand macro="out_l"/>
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79 <expand macro="out_sc"/>
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80 <expand macro="out_sp"/>
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81 <expand macro="out_ss"/>
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82 </outputs>
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83 <tests>
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84 <!--
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85 used in a test:
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86 single library: 12, 1, 2
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87 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
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88 k, phred-offset, disablerr, iontorrent, careful, isolate, only-assembler, only-error-correction, sc
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89
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90 not used in a test:
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
91 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
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
92 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
93
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
94 <!-- #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
95 <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
96 <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
97 <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
98 <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
99 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
100 <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
101 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
102 <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
103 <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
104 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
105 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
106 <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
107 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
108 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
109 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
110 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
111 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
112 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
113 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
114 <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
115 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
116 <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
117 <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
118 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
119 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
120 <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
121 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
122 <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
123 <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
124 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
125 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
126 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
127 <!-- #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
128 <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
129 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
130 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
131 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
132 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
133 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
134 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
135 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
136 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
137 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
138 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
139 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
140 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
141 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
142 <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
143 <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
144 <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
145 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
146 <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
147 <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
148 <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
149 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
150 <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
151 <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
152 <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
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="36"/>
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=">EDGE_.+"/>
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_ags">
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>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
160 <has_n_lines n="2"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
161 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
162 <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
163 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
164 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
165 <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
166 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
167 <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
168 <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
169 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
170 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
171 <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
172 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
173 <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
174 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
175 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
176 <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
177 <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
178 <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
179 <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
180 <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
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 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
183 <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
184 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
185 <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
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 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
188 <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
189 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
190 <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
191 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
192 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
193 <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
194 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
195 <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
196 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
197 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
198 <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
199 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
200 <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
201 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
202 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
203 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
204 <!-- #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
205 <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
206 <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
207 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
208 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
209 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
210 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
211 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
212 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
213 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
214 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
215 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
216 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
217 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
218 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
219 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
220 <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
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 <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
223 <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
224 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
225 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
226 <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
227 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
228 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
229 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
230 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
231 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
232 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
233 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
234 <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
235 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
236 <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
237 <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
238 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
239 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
240 <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
241 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
242 <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
243 <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
244 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
245 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
246 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
247 <!-- #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
248 <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
249 <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
250 <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
251 <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
252 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
253 <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
254 <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
255 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
256 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
257 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
258 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
259 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
260 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
261 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
262 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
263 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
264 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
265 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
266 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
267 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
268 </conditional>
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="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
270 <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
271 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
272 <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
273 <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
274 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
275 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
276 <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
277 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
278 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
279 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
280 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
281 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
282 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
283 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
284 <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
285 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
286 <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
287 <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
288 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
289 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
290 <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
291 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
292 <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
293 <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
294 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
295 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
296 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
297 <!-- #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
298 <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
299 <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
300 <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
301 <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
302 <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
303 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
304 <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
305 <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
306 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
307 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
308 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
309 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
310 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
311 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
312 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
313 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
314 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
315 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
316 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
317 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
318 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
319 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
320 <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
321 <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
322 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
323 <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
324 <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
325 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
326 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
327 <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
328 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
329 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
330 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
331 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
332 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
333 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
334 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
335 <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
336 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
337 <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
338 <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
339 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
340 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
341 <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
342 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
343 <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
344 <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
345 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
346 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
347 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
348 <!-- #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
349 <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
350 <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
351 <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
352 <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
353 <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
354 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
355 <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
356 <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
357 <output_collection name="out_cr" type="list" count="3">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
358 <element name="ecoli_1K.fastq.gz_100.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
359 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
360 <has_size value="130317" delta="7000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
361 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
362 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
363 <element name="ecoli_1K.fastq.gz_200.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
364 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
365 <has_size value="130317" delta="7000"/>
14
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 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
368 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
369 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
370 <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
371 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
372 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
373 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
374 <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
375 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
376 <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
377 </assert_contents>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340
iuc
parents: 5
diff changeset
378 </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
379 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
380 <!-- #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
381 <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
382 <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
383 <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
384 <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
385 <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
386 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
387 <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
388 <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
389 <output_collection name="out_cr" type="list" count="3">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
390 <element name="ecoli_1K.fastq.gz_100.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
391 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
392 <has_size value="130317" delta="7000"/>
14
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 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
395 <element name="ecoli_1K.fastq.gz_200.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
396 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
397 <has_size value="130317" delta="7000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
398 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
399 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
400 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
401 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
402 <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
403 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
404 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
405 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
406 <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
407 <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
408 <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
409 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
410 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
411 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
412 <!-- #8 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
413 <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
414 <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
415 <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
416 <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
417 <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
418 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
419 <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
420 <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
421 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
422 <has_n_lines n="36"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
423 <has_text_matching expression=">EDGE_[0-9]+_length_[0-9]+_cov_[0-9]+\.[0-9]+"/>
14
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 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
426 <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
427 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
428 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
429 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
430 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
431 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
432 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
433 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
434 <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
435 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
436 <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
437 <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
438 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
439 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
440 <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
441 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
442 <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
443 <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
444 </assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
445 </output>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
446 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
447 <!-- #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
448 <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
449 <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
450 <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
451 <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
452 <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
453 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
454 <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
455 <output_collection name="out_cr" type="list" count="3">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
456 <element name="ecoli_1K.fastq.gz_100.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
457 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
458 <has_size value="130317" delta="7000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
459 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
460 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
461 <element name="ecoli_1K.fastq.gz_200.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
462 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
463 <has_size value="130317" delta="7000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
464 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
465 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
466 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
467 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
468 <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
469 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
470 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
471 </output_collection>
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_l">
9
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
473 <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
474 <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
475 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
476 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
477 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
478 <!-- #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
479 <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
480 <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
481 <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
482 <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
483 <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
484 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
485 <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
486 <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
487 <output_collection name="out_cr" type="list" count="3">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
488 <element name="ecoli_1K.fastq.gz_100.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
489 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
490 <has_size value="130317" delta="7000"/>
14
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 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
493 <element name="ecoli_1K.fastq.gz_200.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
494 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
495 <has_size value="130317" delta="7000"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
496 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
497 </element>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
498 <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
499 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
500 <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
501 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
502 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
503 </output_collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
504 <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
505 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
506 <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
507 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
508 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
509 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
510 <!-- #11 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
511 <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
512 <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
513 <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
514 <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
515 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
516 <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
517 <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
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="36"/>
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=">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
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_ags">
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>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
525 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
526 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
527 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
528 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
529 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
530 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
531 <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
532 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
533 <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
534 <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
535 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
536 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
537 <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
538 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
539 <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
540 <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
541 </assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
542 </output>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 8
diff changeset
543 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
544 <!-- #12 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
545 <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
546 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
547 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
548 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
549 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
550 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
551 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
552 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
553 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
554 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
555 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
556 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
557 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
558 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
559 <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
560 <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
561 <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
562 <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
563 <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
564 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
565 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
566 <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
567 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
568 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
569 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
570 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
571 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
572 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
573 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
574 <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
575 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
576 <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
577 <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
578 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
579 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
580 <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
581 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
582 <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
583 <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
584 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
585 </output>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
586 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
587 <!-- #13 -->
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
588 <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
589 <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
590 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
591 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
592 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
593 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
594 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
595 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
596 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
597 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
598 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
599 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
600 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
601 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
602 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
603 <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
604 <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
605 <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
606 <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
607 <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
608 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
609 </output>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
610 <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
611 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
612 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
613 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
614 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
615 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
616 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
617 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
618 <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
619 <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
620 <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
621 <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
622 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
623 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
624 <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
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 <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
627 <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
628 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
629 </output>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
630 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
631 <!-- #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
632 <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
633 <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
634 <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
635 <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
636 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
637 <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
638 <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
639 <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
640 <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
641 <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
642 </section>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
643 <assert_command>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
644 <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
645 <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
646 <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
647 <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
648 </assert_command>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
649 <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
650 <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
651 <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
652 <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
653 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
654 </output>
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_ags">
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>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
657 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
658 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
659 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
660 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
661 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
662 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
663 <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
664 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
665 <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
666 <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
667 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
668 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
669 <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
670 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
671 <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
672 <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
673 </assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
674 </output>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
675 </test>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
676 <!-- #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
677 <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
678 <conditional name="singlePaired">
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
679 <param name="sPaired" value="paired_collection"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
680 <param name="input">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
681 <collection type="list:paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
682 <element name="ecoli_1K">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
683 <collection type="paired">
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
684 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
685 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
686 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
687 </element>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
688 </collection>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
689 </param>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
690 <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
691 <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
692 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
693 <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
694 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
695 <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
696 <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
697 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
698 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
699 <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
700 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
701 <has_n_lines n="2"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
702 <has_text_matching expression="H.+"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
703 <has_text_matching expression="S.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
704 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
705 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
706 <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
707 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
708 <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
709 <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
710 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
711 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
712 <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
713 <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
714 <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
715 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
716 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
717 </test>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
718 <!-- #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
719 <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
720 <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
721 <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
722 <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
723 <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
724 <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
725 <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
726 <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
727 <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
728 </collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
729 </element>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
730 </collection>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
731 </param>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
732 <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
733 </conditional>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
734 <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
735 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
736 <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
737 <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
738 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
739 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
740 <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
741 <assert_contents>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
742 <has_n_lines n="3"/>
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
743 <has_text_matching expression="H.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
744 <has_text_matching expression="S.+"/>
26
b512435320e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 24
diff changeset
745 <has_text_matching expression="P.+"/>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
746 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
747 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
748 <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
749 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
750 <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
751 <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
752 </assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
753 </output>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
754 <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
755 <assert_contents>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
756 <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
757 <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
758 </assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
759 </output>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
iuc
parents: 9
diff changeset
760 </test>
20
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
761 <!-- #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
762 <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
763 <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
764 <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
765 <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
766 </conditional>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
767 <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
768 <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
769 <assert_contents>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
770 <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
771 <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
772 <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
773 </assert_contents>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
774 </output>
78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 19
diff changeset
775 </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
776 </tests>
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
777 <help><![CDATA[
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
778 .. class:: infomark
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
779
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
780 **What it does**
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
781
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
782 @HELP_WID@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
783
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
784 **Input**
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
785
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
786 @HELP_IN@
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
787
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
788 **Output**
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
789
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
790 @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
791 @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
792 @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
793 @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
794 @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
795 @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
796 @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
797 @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
798 @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
799 @HELP_OUT_SS@
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
800
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
801
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
802 -------------------
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
803
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
804 .. class:: infomark
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
805
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
806 **IonTorrent data**
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
807
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
808 @IONTORRENT@
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
809
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
810 -------------------
7
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25
iuc
parents: 6
diff changeset
811
14
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
812 .. class:: infomark
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
813
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
814 **References**
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
815
21
a789e163a670 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 20
diff changeset
816 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
817 ]]></help>
74f20c988994 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 13
diff changeset
818 <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
819 <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
820 <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
821 </expand>
0
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
822 </tool>