Mercurial > repos > iuc > rnaspades

annotate rnaspades.xml @ 16:9c943a025be3 draft default tip

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 2cc77819587d2ecaf4ce7f12e0bf8b17e125a9d8
author iuc
date Mon, 12 May 2025 06:59:48 +0000
parents 3da6bde1f252
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
1 <tool id="rnaspades" name="rnaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
2 <description>de novo transcriptome assembler</description>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
3 <macros>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
4 <import>macros.xml</import>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
5 </macros>
14
83b3744d6ced planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390
iuc
parents: 12
diff changeset
6 <xrefs>
83b3744d6ced planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390
iuc
parents: 12
diff changeset
7 <xref type="bio.tools">rnaspades</xref>
83b3744d6ced planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390
iuc
parents: 12
diff changeset
8 </xrefs>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
9 <expand macro="requirements"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
10 <expand macro="stdio"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
11 <expand macro="version_command"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
2
5c7a049d755b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit b7a410ba698811d0b903b3c72191ae6564bf5a8c"
iuc
parents: 1
diff changeset
13
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
14 #set $library = 1
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
15
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
16 @PREPROCESS_INPUT_FILES_MAIN@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
17 #if $additional_reads.selector == 'true'
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
18 @PREPROCESS_INPUT_FILES_ADDITIONAL@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
19 #end if
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
20 @PREPROCESS_NANOPORE_PACBIO_FILES@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
21 @PREPROCESS_CONTIGS_FILES@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
22 @PREPROCESS_FL_RNA_FILES@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
23
12
dbe8105ae7a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 7
diff changeset
24 @OMP_THREADS@
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
25 ## run
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
26 rnaspades.py
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
27 -o 'output'
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
28 @RESOURCES@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
29 @INPUT_READS_MAIN@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
30 #if $additional_reads.selector == 'true'
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
31 @INPUT_READS_ADDITIONAL@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
32 #end if
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
33 ## additional reads
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
34 @FL_RNA@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
35 @NANOPORE_PACBIO@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
36 @CONTIGS@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
37 ## parameter
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
38 @KMER@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
39 @PIPELINE_OPTIONS@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
40 @PHREDOFFSET@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
41 #if $ss != 'no'
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
42 --ss '$ss'
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
43 #end if
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
44 ## postprocessing
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
45 ]]></command>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
46 <inputs>
15
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
47 <expand macro="input_files_all" format="@INTYPES@" label="FASTQ RNA-seq file(s)"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
48 <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTQ RNA-seq file(s)"/>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
49 <section name="arf" title="Additional read files">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
50 <expand macro="flrna"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
51 <expand macro="nanopore_pacbio"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
52 <expand macro="contigs"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
53 </section>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
54 <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."/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
55 <expand macro="phred"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
56 <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">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
57 <option value="no" selected="true">Disabled</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
58 <option value="fr">FR (normal)</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
59 <option value="rf">RF (antisense)</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
60 </param>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
61 <expand macro="pipeline_options">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
62 <option value="--iontorrent">Iontorrent: although rnaSPAdes supports IonTorrent reads, it was not sufficiently tested on such kind of data (--iontorrent)</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
63 </expand>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
64 <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.">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
65 <option value="hft">Hard filtered transcripts</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
66 <option value="l">Log</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
67 <option value="sft">Soft filtered transcripts</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
68 <option value="tr" selected="true">Transcripts</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
69 <option value="tp">Transcripts paths</option>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
70 </param>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
71 </inputs>
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
72 <outputs>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
73 <expand macro="out_cr"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
74 <data name="out_hft" format="fasta" from_work_dir="output/hard_filtered_transcripts.fasta" label="${tool.name} on ${on_string}: Hard filtered transcripts">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
75 <filter>'hft' in optional_output</filter>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
76 </data>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
77 <expand macro="out_l"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
78 <data name="out_sft" format="fasta" from_work_dir="output/soft_filtered_transcripts.fasta" label="${tool.name} on ${on_string}: Soft filtered transcripts">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
79 <filter>'sft' in optional_output</filter>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
80 </data>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
81 <data name="out_tr" format="fasta" from_work_dir="output/transcripts.fasta" label="${tool.name} on ${on_string}: Transcripts">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
82 <filter>'tr' in optional_output</filter>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
83 </data>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
84 <data name="out_tp" format="txt" from_work_dir="output/transcripts.paths" label="${tool.name} on ${on_string}: Transcripts paths">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
85 <filter>'tp' in optional_output</filter>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
86 </data>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
87 </outputs>
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
88 <tests>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
89 <!--
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
90 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
91 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
92 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
93
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
94 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
95 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
96 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
97 -->
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 <!-- #1 -->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
100 <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
101 <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
102 <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
103 <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
104 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
105 <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
106 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
107 <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
108 <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
109 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
110 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
111 </test>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
112 <!-- #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
113 <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
114 <conditional name="singlePaired">
15
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
115 <param name="sPaired" value="paired_collection"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
116 <param name="input">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
117 <collection type="list:paired">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
118 <element name="ecoli_1K">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
119 <collection type="paired">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
120 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
121 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
122 </collection>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
123 </element>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
124 </collection>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
125 </param>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
126 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
127 <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
128 <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
129 <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
130 <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
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 <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
133 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
134 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
135 <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
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 <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
138 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
139 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
140 <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
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 <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
143 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
144 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
145 <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
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 <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
148 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
149 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
150 <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
151 <assert_contents>
15
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
152 <has_text_matching expression="Thank you for using rnaSPAdes!"/>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
153 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
154 </output>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
155 </test>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
156 <!-- #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
157 <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
158 <conditional name="singlePaired">
15
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
159 <param name="sPaired" value="paired_collection"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
160 <param name="input">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
161 <collection type="list:paired">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
162 <element name="ecoli_1K">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
163 <collection type="paired">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
164 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
165 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
166 </collection>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
167 </element>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
168 </collection>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
169 </param>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
170 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
171 <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
172 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
173 <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
174 <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
175 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
176 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
177 </test>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
178 <!-- #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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 <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
187 <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
188 </collection>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
189 </element>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
190 </collection>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
191 </param>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
192 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
193 <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
194 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
195 <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
196 <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
197 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
198 </output>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
199 </test>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
200 <!-- #3 Hibryd assembly -->
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
201 <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
202 <conditional name="singlePaired">
15
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
203 <param name="sPaired" value="paired_collection"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
204 <param name="input">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
205 <collection type="list:paired">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
206 <element name="ecoli_1K">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
207 <collection type="paired">
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
208 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
209 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
210 </collection>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
211 </element>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
212 </collection>
3da6bde1f252 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
iuc
parents: 14
diff changeset
213 </param>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
214 </conditional>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
215 <section name="arf">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
216 <param name="nanopore" 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
217 <param name="pacbio" 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
218 <param name="trusted_contigs" value="ecoli_1K.fasta.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
219 <param name="flrna" value="ecoli_1K.fasta.gz"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
220 </section>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
221 <assert_command>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
222 <has_text text="--nanopore"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
223 <has_text text="--pacbio"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
224 <has_text text="--trusted-contigs"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
225 <has_text text="--fl-rna"/>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
226 </assert_command>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
227 <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
228 <assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
229 <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
230 <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
231 </assert_contents>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
232 </output>
3
cc958b392637 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 2
diff changeset
233 </test>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
234 </tests>
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
235 <help><![CDATA[
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
236 .. class:: infomark
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
237
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
238 **What it does**
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
239
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
240 @HELP_WID@
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
241
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
242 rnaSPAdes is a subtool for de novo transcriptome assembly from RNA-Seq data and is suitable for all kinds of organisms.
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
243
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
244 **Input**
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
245
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
246 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.
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
247
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
248 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,
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
249 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
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
250 and strand-specificity. Transcript quantification for each sample can be done afterwards by separately mapping reads from each library to the assembled transcripts.
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
251
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
252 **Output**
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
253
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
254 @HELP_OUT_AG@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
255 @HELP_OUT_AGS@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
256 @HELP_OUT_CR@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
257 - Hard filtered transcripts includes only long and reliable transcripts with rather high expression
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
258 @HELP_OUT_L@
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
259 - Soft filtered transcripts includes short and low-expressed transcipts, likely to contain junk sequences
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
260 - Transcripts
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
261 - Transcripts paths
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
262
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
263 .. class:: infomark
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
264
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
265 **References**
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
266
12
dbe8105ae7a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 7
diff changeset
267 More information can be found on on `github <https://github.com/ablab/spades>`_.
7
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
268 ]]></help>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
269 <expand macro="citations">
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
270 <citation type="doi">10.1101/420208</citation>
554afb32acff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9300c35493d87bab1080cb935b27787addc5b36e"
iuc
parents: 6
diff changeset
271 </expand>
0
a3e9e9b63502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff changeset
272 </tool>