Mercurial > repos > nml > metaspades

annotate metaspades.xml @ 6:a9b8c9e204ee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author iuc
date Sun, 23 Jan 2022 21:33:56 +0000
parents 3ca2d2a9068c
children f338e9942b27
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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1 <tool id="metaspades" name="metaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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2 <description>metagenome assembler</description>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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9 <command detect_errors="exit_code"><![CDATA[
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10
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11 #set $library = 1
3
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12
6
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13 @PREPROCESS_INPUT_FILES_MAIN@
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14 #if $additional_reads.selector == 'true'
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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15 @PREPROCESS_INPUT_FILES_ADDITIONAL@
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16 #end if
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17 @PREPROCESS_NANOPORE_PACBIO_FILES@
3
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18
6
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19 ## run
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20 metaspades.py
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21 -o 'output'
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22 @RESOURCES@
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23 @INPUT_READS_MAIN@
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24 #if $additional_reads.selector == 'true'
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25 @INPUT_READS_ADDITIONAL@
1
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26 #end if
6
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27 ## reads
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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28 @NANOPORE_PACBIO@
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29 ## parameter
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30 @KMER@
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31 @PHREDOFFSET@
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32 @PIPELINE_OPTIONS@
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33 ## postprocessing
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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34 @STATS@
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35 @CORRECTED@
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36 ]]></command>
1
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37 <inputs>
6
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38 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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39 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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40 <section name="arf" title="Additional read files">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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41 <expand macro="nanopore_pacbio"/>
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42 </section>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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43 <section name="arf" title="Additional read files">
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44 <expand macro="nanopore_pacbio"/>
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45 </section>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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46 <expand macro="kmer"/>
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47 <expand macro="phred"/>
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48 <expand macro="pipeline_options">
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49 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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50 </expand>
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51 <expand macro="optional_output"/>
1
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52 </inputs>
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53 <outputs>
6
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54 <expand macro="out_ag"/>
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55 <expand macro="out_ags"/>
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56 <expand macro="out_cn"/>
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57 <expand macro="out_cp"/>
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58 <expand macro="out_cr"/>
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59 <expand macro="out_cs"/>
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60 <expand macro="out_l"/>
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61 <expand macro="out_sc"/>
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62 <expand macro="out_sp"/>
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63 <expand macro="out_ss"/>
1
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64 </outputs>
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65 <tests>
6
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66 <!-- #1 single, interlaced, fastq.gz, default parameters -->
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67 <test expect_num_outputs="4">
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68 <conditional name="singlePaired">
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69 <param name="sPaired" value="paired_interlaced"/>
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70 <param name="input1" value="ecoli_1K.fastq.gz"/>
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71 </conditional>
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72 <output name="out_ag">
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73 <assert_contents>
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74 <has_n_lines n="36"/>
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75 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106'"/>
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76 </assert_contents>
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77 </output>
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78 <output name="out_ags">
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79 <assert_contents>
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80 <has_n_lines n="2"/>
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81 <has_text_matching expression="S.+"/>
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82 </assert_contents>
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83 </output>
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84 <output name="out_cn">
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85 <assert_contents>
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86 <has_n_lines n="18"/>
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87 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
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88 </assert_contents>
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89 </output>
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90 <output name="out_sc">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
91 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
92 <has_n_lines n="18"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
93 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
94 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
95 </output>
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
96 </test>
6
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
97 <!-- #2 single, separate, fastq, default parameters -->
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
98 <test expect_num_outputs="4">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
99 <conditional name="singlePaired">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
100 <param name="sPaired" value="paired"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
101 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
102 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
103 </conditional>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
104 <output name="out_ag">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
105 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
106 <has_n_lines n="36"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
107 <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106'"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
108 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
109 </output>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
110 <output name="out_ags">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
111 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
112 <has_n_lines n="2"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
113 <has_text_matching expression="S.+"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
114 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
115 </output>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
116 <output name="out_cn">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
117 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
118 <has_n_lines n="18"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
119 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
120 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
121 </output>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
122 <output name="out_sc">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
123 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
124 <has_n_lines n="18"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
125 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
126 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
127 </output>
4
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
128 </test>
6
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
129 <!-- #3 only corrected reads are created as an output -->
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
130 <test expect_num_outputs="2">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
131 <conditional name="singlePaired">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
132 <param name="sPaired" value="paired_interlaced"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
133 <param name="input1" value="ecoli_1K.fastq.gz"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
134 </conditional>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
135 <param name="optional_output" value="cr,l"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
136 <output_collection name="out_cr" type="list" count="3">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
137 <element name="ecoli_1K.fastq.gz_1.00.0_0.cor">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
138 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
139 <has_size value="130317" delta="1000"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
140 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
141 </element>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
142 <element name="ecoli_1K.fastq.gz_2.00.0_0.cor">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
143 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
144 <has_size value="130317" delta="1000"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
145 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
146 </element>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
147 <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
148 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
149 <has_size value="20" delta="5"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
150 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
151 </element>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
152 </output_collection>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
153 <output name="out_l">
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
154 <assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
155 <has_text_matching expression="Thank you for using SPAdes!"/>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
156 </assert_contents>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
157 </output>
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
158 </test>
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
159 </tests>
6
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
160 <help><![CDATA[
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
161 .. class:: infomark
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
162
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
163 **What it does**
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
164
6
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
165 @HELP_WID@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
166
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
167 metaSPAdes is a subtool for assembling metagenomic data sets.
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
168
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
169 **Input**
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
170
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
171 @HELP_IN@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
172
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
173 **Output**
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
174
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
175 @HELP_OUT_AG@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
176 @HELP_OUT_AGS@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
177 @HELP_OUT_C@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
178 @HELP_OUT_CP@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
179 @HELP_OUT_CR@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
180 @HELP_OUT_CS@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
181 @HELP_OUT_L@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
diff changeset
182 @HELP_OUT_S@
a9b8c9e204ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents: 5
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183 @HELP_OUT_SP@
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184 @HELP_OUT_SS@
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185
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186 **References**
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187
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188 More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/meta-spades>`_.
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189 ]]></help>
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190 <expand macro="citations">
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191 <citation type="doi">10.1101/gr.213959.116</citation>
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192 </expand>
0
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193 </tool>