Mercurial > repos > iuc > rnaspades
annotate rnaspades.xml @ 14:5fc94b3a4704 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f53f7f297e551bf58e753752edd0dae5205bbc77
author | iuc |
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date | Mon, 15 Apr 2024 19:38:38 +0000 |
parents | 28189050e437 |
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rev | line source |
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6
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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1 <tool id="rnaspades" name="rnaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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2 <description>de novo transcriptome assembler</description> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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3 <macros> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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4 <import>macros.xml</import> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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5 </macros> |
13
28189050e437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
iuc
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6 <xrefs> |
28189050e437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
iuc
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7 <xref type="bio.tools">rnaspades</xref> |
28189050e437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
iuc
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8 </xrefs> |
6
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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9 <expand macro="requirements"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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10 <expand macro="stdio"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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11 <expand macro="version_command"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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12 <command detect_errors="exit_code"><![CDATA[ |
2
03fd468e158f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit b7a410ba698811d0b903b3c72191ae6564bf5a8c"
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13 |
6
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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14 #set $library = 1 |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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15 |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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16 @PREPROCESS_INPUT_FILES_MAIN@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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17 #if $additional_reads.selector == 'true' |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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18 @PREPROCESS_INPUT_FILES_ADDITIONAL@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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19 #end if |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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20 @PREPROCESS_NANOPORE_PACBIO_FILES@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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21 @PREPROCESS_CONTIGS_FILES@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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22 @PREPROCESS_FL_RNA_FILES@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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23 |
11
675ee1aa5952
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
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24 @OMP_THREADS@ |
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b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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25 ## run |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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26 rnaspades.py |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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27 -o 'output' |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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28 @RESOURCES@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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29 @INPUT_READS_MAIN@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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30 #if $additional_reads.selector == 'true' |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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31 @INPUT_READS_ADDITIONAL@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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32 #end if |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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33 ## additional reads |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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34 @FL_RNA@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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35 @NANOPORE_PACBIO@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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36 @CONTIGS@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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37 ## parameter |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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38 @KMER@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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39 @PIPELINE_OPTIONS@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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40 @PHREDOFFSET@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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41 #if $ss != 'no' |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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42 --ss '$ss' |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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43 #end if |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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44 ## postprocessing |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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45 @CORRECTED@ |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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46 ]]></command> |
0
0d30fed9628b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
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47 <inputs> |
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b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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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)"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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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)"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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50 <section name="arf" title="Additional read files"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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51 <expand macro="flrna"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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52 <expand macro="nanopore_pacbio"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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53 <expand macro="contigs"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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54 </section> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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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."/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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56 <expand macro="phred"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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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"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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58 <option value="no" selected="true">Disabled</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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59 <option value="fr">FR (normal)</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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60 <option value="rf">RF (antisense)</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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61 </param> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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62 <expand macro="pipeline_options"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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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> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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64 </expand> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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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."> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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66 <option value="hft">Hard filtered transcripts</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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67 <option value="l">Log</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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68 <option value="sft">Soft filtered transcripts</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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69 <option value="tr" selected="true">Transcripts</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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70 <option value="tp">Transcripts paths</option> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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71 </param> |
0
0d30fed9628b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
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72 </inputs> |
0d30fed9628b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
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73 <outputs> |
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b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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74 <expand macro="out_cr"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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75 <data name="out_hft" format="fasta" from_work_dir="output/hard_filtered_transcripts.fasta" label="${tool.name} on ${on_string}: Hard filtered transcripts"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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76 <filter>'hft' in optional_output</filter> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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77 </data> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
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78 <expand macro="out_l"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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diff
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|
79 <data name="out_sft" format="fasta" from_work_dir="output/soft_filtered_transcripts.fasta" label="${tool.name} on ${on_string}: Soft filtered transcripts"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
80 <filter>'sft' in optional_output</filter> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
81 </data> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
82 <data name="out_tr" format="fasta" from_work_dir="output/transcripts.fasta" label="${tool.name} on ${on_string}: Transcripts"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
83 <filter>'tr' in optional_output</filter> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
84 </data> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
85 <data name="out_tp" format="txt" from_work_dir="output/transcripts.paths" label="${tool.name} on ${on_string}: Transcripts paths"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
86 <filter>'tp' in optional_output</filter> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
87 </data> |
0
0d30fed9628b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff
changeset
|
88 </outputs> |
0d30fed9628b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff
changeset
|
89 <tests> |
6
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
90 <!-- |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
91 used in a test: |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
92 single library: 12, 1, 2 |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
93 k, phred-offset, disablerr, iontorrent, only-assembler, ss |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
94 |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
95 not used in a test: |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
96 single library: merged, s |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
97 pacbio, nanopore, trusted-contigs, untrusted-contigs, fl-rna |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
98 --> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
99 |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
100 <!-- #1 --> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
101 <test expect_num_outputs="1"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
102 <conditional name="singlePaired"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
103 <param name="sPaired" value="paired_interlaced"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
104 <param name="input1" value="ecoli_1K.fastq.gz"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
105 </conditional> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
106 <output name="out_tr"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
107 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
108 <has_n_lines n="18"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
109 <has_text_matching expression=">NODE\_1\_length\_1000.+"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
110 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
111 </output> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
112 </test> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
113 <!-- #2 single, separate, fastq, all outputs custom parameters--> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
114 <test expect_num_outputs="5"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
115 <conditional name="singlePaired"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
116 <param name="sPaired" value="paired"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
117 <param name="input1" value="ecoli_1K_1.fastq.gz"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
118 <param name="input2" value="ecoli_1K_2.fastq.gz"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
119 </conditional> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
120 <param name="phred_offset" value="33"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
121 <param name="ss" value="fr"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
122 <param name="optional_output" value="hft,l,sft,tr,tp"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
123 <output name="out_hft"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
124 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
125 <has_n_lines n="18"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
126 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
127 </output> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
128 <output name="out_sft"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
129 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
130 <has_n_lines n="18"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
131 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
132 </output> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
133 <output name="out_tr"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
134 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
135 <has_n_lines n="18"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
136 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
137 </output> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
138 <output name="out_tp"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
139 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
140 <has_n_lines n="4"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
141 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
142 </output> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
143 <output name="out_l"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
144 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
145 <has_text_matching expression="Thank you for using SPAdes!"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
146 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
147 </output> |
0
0d30fed9628b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
iuc
parents:
diff
changeset
|
148 </test> |
6
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
149 <!-- #3 single, separate, fasta, default parameters --> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
150 <test expect_num_outputs="1"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
151 <conditional name="singlePaired"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
152 <param name="sPaired" value="paired"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
153 <param name="input1" value="ecoli_1K_1.fasta.gz"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
154 <param name="input2" value="ecoli_1K_2.fasta.gz"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
155 </conditional> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
156 <output name="out_tr"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
157 <assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
158 <has_n_lines n="18"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
159 <has_text_matching expression=">NODE\_1\_length\_1000.+"/> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
5
diff
changeset
|
160 </assert_contents> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
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161 </output> |
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162 </test> |
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163 <!-- #3 Collection, default parameters --> |
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164 <test expect_num_outputs="1"> |
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165 <conditional name="singlePaired"> |
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166 <param name="sPaired" value="paired_collection"/> |
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167 <param name="input"> |
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168 <collection type="list:paired"> |
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169 <element name="ecoli.fastq"> |
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170 <collection type="paired"> |
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171 <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/> |
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172 <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/> |
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173 </collection> |
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174 </element> |
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175 </collection> |
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176 </param> |
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177 </conditional> |
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178 <output name="out_tr"> |
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179 <assert_contents> |
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180 <has_n_lines n="18"/> |
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181 <has_text_matching expression=">NODE\_1\_length\_1000.+"/> |
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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> |
6
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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 |
6
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217 @HELP_WID@ |
0
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218 |
6
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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 |
6
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221 **Input** |
0
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222 |
6
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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. |
0
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224 |
6
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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 |
6
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229 **Output** |
0
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230 |
6
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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 |
6
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240 .. class:: infomark |
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241 |
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242 **References** |
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243 |
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675ee1aa5952
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
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244 More information can be found on on `github <https://github.com/ablab/spades>`_. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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245 ]]></help> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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246 <expand macro="citations"> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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247 <citation type="doi">10.1101/420208</citation> |
b66de1e9abfb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
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248 </expand> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 9bfb3d0e41daa3990a997b92438b9e56c2b6edbf
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249 </tool> |