Mercurial > repos > iuc > rnaspades

annotate rnaspades.xml @ 14:83b3744d6ced draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390
author iuc
date Mon, 03 Mar 2025 11:05:55 +0000
parents dbe8105ae7a1
children 3da6bde1f252
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1 <tool id="rnaspades" name="rnaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>de novo transcriptome assembler</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">rnaspades</xref>
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8 </xrefs>
7
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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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14 #set $library = 1
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16 @PREPROCESS_INPUT_FILES_MAIN@
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17 #if $additional_reads.selector == 'true'
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18 @PREPROCESS_INPUT_FILES_ADDITIONAL@
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19 #end if
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20 @PREPROCESS_NANOPORE_PACBIO_FILES@
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21 @PREPROCESS_CONTIGS_FILES@
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22 @PREPROCESS_FL_RNA_FILES@
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23
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24 @OMP_THREADS@
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25 ## run
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26 rnaspades.py
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27 -o 'output'
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28 @RESOURCES@
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29 @INPUT_READS_MAIN@
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30 #if $additional_reads.selector == 'true'
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31 @INPUT_READS_ADDITIONAL@
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32 #end if
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33 ## additional reads
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34 @FL_RNA@
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35 @NANOPORE_PACBIO@
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36 @CONTIGS@
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37 ## parameter
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38 @KMER@
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39 @PIPELINE_OPTIONS@
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40 @PHREDOFFSET@
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41 #if $ss != 'no'
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42 --ss '$ss'
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43 #end if
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44 ## postprocessing
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45 @CORRECTED@
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46 ]]></command>
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47 <inputs>
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48 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
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49 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
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50 <section name="arf" title="Additional read files">
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51 <expand macro="flrna"/>
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52 <expand macro="nanopore_pacbio"/>
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53 <expand macro="contigs"/>
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54 </section>
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55 <expand macro="kmer" help="By default rnaSPAdes uses 2 k-mer sizes, which are automatically detected using read length (approximately one third and half of the maximal read length). We recommend not to change this parameter because smaller k-mer sizes typically result in multiple chimeric (misassembled) transcripts."/>
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56 <expand macro="phred"/>
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57 <param argument="--ss" type="select" label="Set strand specificity" help="rnaSPAdes supports strand-specific RNA-Seq datasets. Use 'RF' when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and 'FR' otherwise. If the dataset is single-end use 'FR' option in case when reads correspond to gene strand and 'RF' otherwise. Note: strand-specificity is not related and should not be confused with FR and RF orientation of paired reads. RNA-Seq paired-end reads typically have forward-reverse orientation, which is assumed by default and no additional options are needed">
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58 <option value="no" selected="true">Disabled</option>
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59 <option value="fr">FR (normal)</option>
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60 <option value="rf">RF (antisense)</option>
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61 </param>
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62 <expand macro="pipeline_options">
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63 <option value="--iontorrent">Iontorrent: although rnaSPAdes supports IonTorrent reads, it was not sufficiently tested on such kind of data (--iontorrent)</option>
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64 </expand>
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65 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run.">
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66 <option value="hft">Hard filtered transcripts</option>
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67 <option value="l">Log</option>
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68 <option value="sft">Soft filtered transcripts</option>
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69 <option value="tr" selected="true">Transcripts</option>
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70 <option value="tp">Transcripts paths</option>
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71 </param>
0
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72 </inputs>
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73 <outputs>
7
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74 <expand macro="out_cr"/>
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75 <data name="out_hft" format="fasta" from_work_dir="output/hard_filtered_transcripts.fasta" label="${tool.name} on ${on_string}: Hard filtered transcripts">
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76 <filter>'hft' in optional_output</filter>
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77 </data>
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78 <expand macro="out_l"/>
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79 <data name="out_sft" format="fasta" from_work_dir="output/soft_filtered_transcripts.fasta" label="${tool.name} on ${on_string}: Soft filtered transcripts">
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80 <filter>'sft' in optional_output</filter>
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81 </data>
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82 <data name="out_tr" format="fasta" from_work_dir="output/transcripts.fasta" label="${tool.name} on ${on_string}: Transcripts">
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83 <filter>'tr' in optional_output</filter>
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84 </data>
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85 <data name="out_tp" format="txt" from_work_dir="output/transcripts.paths" label="${tool.name} on ${on_string}: Transcripts paths">
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86 <filter>'tp' in optional_output</filter>
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87 </data>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
88 </outputs>
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
89 <tests>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
90 <!--
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
91 used in a test:
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
92 single library: 12, 1, 2
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
93 k, phred-offset, disablerr, iontorrent, only-assembler, ss
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
94
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
95 not used in a test:
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
96 single library: merged, s
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
97 pacbio, nanopore, trusted-contigs, untrusted-contigs, fl-rna
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
98 -->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
99
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
100 <!-- #1 -->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
101 <test expect_num_outputs="1">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
102 <conditional name="singlePaired">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
103 <param name="sPaired" value="paired_interlaced"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
104 <param name="input1" value="ecoli_1K.fastq.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
105 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
106 <output name="out_tr">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
107 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
108 <has_n_lines n="18"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
109 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
110 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
111 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
112 </test>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
113 <!-- #2 single, separate, fastq, all outputs custom parameters-->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
114 <test expect_num_outputs="5">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
115 <conditional name="singlePaired">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
116 <param name="sPaired" value="paired"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
117 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
118 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
119 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
120 <param name="phred_offset" value="33"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
121 <param name="ss" value="fr"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
122 <param name="optional_output" value="hft,l,sft,tr,tp"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
123 <output name="out_hft">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
124 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
125 <has_n_lines n="18"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
126 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
127 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
128 <output name="out_sft">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
129 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
130 <has_n_lines n="18"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
131 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
132 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
133 <output name="out_tr">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
134 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
135 <has_n_lines n="18"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
136 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
137 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
138 <output name="out_tp">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
139 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
140 <has_n_lines n="4"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
141 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
142 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
143 <output name="out_l">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
144 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
145 <has_text_matching expression="Thank you for using SPAdes!"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
146 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
147 </output>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
148 </test>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
149 <!-- #3 single, separate, fasta, default parameters -->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
150 <test expect_num_outputs="1">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
151 <conditional name="singlePaired">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
152 <param name="sPaired" value="paired"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
153 <param name="input1" value="ecoli_1K_1.fasta.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
154 <param name="input2" value="ecoli_1K_2.fasta.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
155 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
156 <output name="out_tr">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
157 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
158 <has_n_lines n="18"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
159 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
160 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
161 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
162 </test>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
163 <!-- #3 Collection, default parameters -->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
164 <test expect_num_outputs="1">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
165 <conditional name="singlePaired">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
166 <param name="sPaired" value="paired_collection"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
167 <param name="input">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
168 <collection type="list:paired">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
169 <element name="ecoli.fastq">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
170 <collection type="paired">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
171 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
172 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
173 </collection>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
174 </element>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
175 </collection>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
176 </param>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
177 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
178 <output name="out_tr">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
179 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
180 <has_n_lines n="18"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
181 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
182 </assert_contents>
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183 </output>
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184 </test>
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185 <!-- #3 Hibryd assembly -->
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186 <test expect_num_outputs="1">
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187 <conditional name="singlePaired">
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188 <param name="sPaired" value="paired"/>
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189 <param name="input1" value="ecoli_1K_1.fasta.gz"/>
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190 <param name="input2" value="ecoli_1K_2.fasta.gz"/>
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191 </conditional>
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192 <section name="arf">
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193 <param name="nanopore" value="ecoli_1K.fastq.gz"/>
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194 <param name="pacbio" value="ecoli_1K.fastq.gz"/>
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195 <param name="trusted_contigs" value="ecoli_1K.fasta.gz"/>
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196 <param name="flrna" value="ecoli_1K.fasta.gz"/>
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197 </section>
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198 <assert_command>
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199 <has_text text="--nanopore"/>
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200 <has_text text="--pacbio"/>
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201 <has_text text="--trusted-contigs"/>
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202 <has_text text="--fl-rna"/>
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203 </assert_command>
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204 <output name="out_tr">
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205 <assert_contents>
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206 <has_n_lines n="18"/>
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207 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
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208 </assert_contents>
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209 </output>
3
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210 </test>
0
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211 </tests>
7
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212 <help><![CDATA[
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213 .. class:: infomark
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214
0
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215 **What it does**
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216
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217 @HELP_WID@
0
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218
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219 rnaSPAdes is a subtool for de novo transcriptome assembly from RNA-Seq data and is suitable for all kinds of organisms.
0
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220
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221 **Input**
0
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222
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223 rnaSPAdes take as an input at least one paired-end or single-end library. For hybrid assembly you can use PacBio or Oxford Nanopore reads.
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224
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225 In case you have sequenced several RNA-Seq libraries using the same protocol from different tissues / conditions, and the goal as to assemble a total transcriptome,
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226 we suggest to provide all files as a single library. Note, that sequencing using the same protocol implies that the resulting reads have the same length, insert size
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227 and strand-specificity. Transcript quantification for each sample can be done afterwards by separately mapping reads from each library to the assembled transcripts.
0
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228
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229 **Output**
0
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230
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231 @HELP_OUT_AG@
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232 @HELP_OUT_AGS@
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233 @HELP_OUT_CR@
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234 - Hard filtered transcripts includes only long and reliable transcripts with rather high expression
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235 @HELP_OUT_L@
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236 - Soft filtered transcripts includes short and low-expressed transcipts, likely to contain junk sequences
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237 - Transcripts
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238 - Transcripts paths
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239
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240 .. class:: infomark
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241
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242 **References**
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243
12
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244 More information can be found on on `github <https://github.com/ablab/spades>`_.
7
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245 ]]></help>
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246 <expand macro="citations">
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247 <citation type="doi">10.1101/420208</citation>
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248 </expand>
0
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249 </tool>