Mercurial > repos > iuc > quast
annotate quast.xml @ 3:6fcbee531de6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
author | iuc |
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date | Fri, 29 Sep 2017 05:51:26 -0400 |
parents | 2f581f956e1c |
children | 0834c823d4b9 |
rev | line source |
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3
6fcbee531de6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
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2
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1 <tool id="quast" name="Quast" version="4.5" > |
0
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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2 <description>Genome assembly Quality</description> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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3 <requirements> |
3
6fcbee531de6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
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2
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4 <requirement type="package" version="4.5">quast</requirement> |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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5 </requirements> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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6 <stdio> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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7 <regex match="ERROR! exception caught!" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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8 source="both" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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9 level="fatal" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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10 description="Something went wrong. Check the following errors : No labels..." /> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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11 </stdio> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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12 <command> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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13 <![CDATA[ |
2
2f581f956e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 930a43568ac0d4d32dde38a56fbb0b826f8f591b
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14 #import re |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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15 quast |
3
6fcbee531de6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
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16 --threads \${GALAXY_SLOTS:-4} |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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17 -o outputdir |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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18 #if $gene_selection == "eukaryote": |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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19 --eukaryote |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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20 #else if $gene_selection == "metagenes": |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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21 --meta |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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22 #end if |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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23 #if $input_ref: |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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24 -R '$input_ref' |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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25 #if $input_operon: |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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26 -O '$input_operon' |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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27 #end if |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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28 #if $annot: |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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29 -G '$annot' |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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30 #end if |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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31 #end if |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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32 #if $input_size: |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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33 --est-ref-size $input_size |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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34 #end if |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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35 --min-contig $min_contig |
1
0edbf19cf5eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8
iuc
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36 -l |
2
2f581f956e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 930a43568ac0d4d32dde38a56fbb0b826f8f591b
iuc
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37 #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) |
3
6fcbee531de6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
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38 |
1
0edbf19cf5eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8
iuc
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39 $names |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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40 --contig-thresholds $threshold_contig |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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41 #for $k in $files: |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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42 #if $k.type_file == "scaffold": |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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43 -s |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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44 #end if |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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45 $k.input |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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46 #end for |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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47 && |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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48 mv outputdir/report.txt '$quast_out' && |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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49 mv outputdir/report.tsv '$quast_tsv' && |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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50 mv outputdir/report.tex '$quast_tex' && |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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51 mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && |
3
6fcbee531de6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
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52 mv outputdir/report.html '$report_html' |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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53 ]]> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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54 </command> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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55 <inputs> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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56 <repeat name="files" title="Input assembly files" min="1"> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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57 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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58 <param name="type_file" type="select" label="Type of data"> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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59 <option value="contig">Contig</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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60 <option value="scaffold">Scaffold</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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61 </param> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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62 </repeat> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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63 <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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64 help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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65 <param name="input_ref" type="data" format="fasta" label="Reference File" optional="True" argument="-R" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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66 help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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67 <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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68 help="File with gene positions in the reference genome. "/> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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69 <param name="input_operon" type="data" format="txt" label="Operon Annotations" optional="True" argument="-O" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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70 help="File with operon positions in the reference genome"/> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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71 <param name="gene_selection" type="select" label="Type of organism"> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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72 <option value="prokaryotes">Prokaryotes</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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73 <option value="eukaryote">Eukaryote</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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74 <option value="metagenes">Metagenomes</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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75 </param> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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76 <param name="min_contig" type="integer" value="500" label="Lower Threshold" argument="--min-contig" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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77 help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account (default is 500)"/> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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78 <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds" |
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79 help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.(default is 0,1000)"/> |
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80 </inputs> |
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81 <outputs> |
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82 <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/> |
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83 <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/> |
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84 <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/> |
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85 <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/> |
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86 <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/> |
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87 </outputs> |
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88 <tests> |
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89 <test> |
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90 <param name="input" value="contigs_1.fasta"/> |
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91 <param name="input.type_file" value="contig"/> |
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92 <param name="gene_selection" value="prokaryotes"/> |
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93 <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> |
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94 </test> |
3
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95 <test> |
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96 <param name="input" value="contigs_1.fasta"/> |
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97 <param name="input.type_file" value="contig"/> |
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98 <param name="input_ref" value="NC000913.3_1-6650.fasta"/> |
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99 <param name="gene_selection" value="prokaryotes"/> |
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100 <output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/> |
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101 </test> |
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102 <test> |
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103 <param name="input" value="contigs_1.fasta"/> |
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104 <param name="input.type_file" value="contig"/> |
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105 <param name="input_ref" value="NC000913.3_1-6650.fasta"/> |
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106 <param name="annot" value="NC000913.3_1-6650.gff"/> |
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107 <param name="gene_selection" value="prokaryotes"/> |
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108 <output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/> |
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109 </test> |
0
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110 </tests> |
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111 <help> |
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112 <![CDATA[ |
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113 **Description** |
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114 |
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115 Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics. |
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116 |
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117 ----- |
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118 |
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119 **Inputs and Outputs** |
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120 |
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121 - Input: |
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122 + The tool accepts assemblies and references in FASTA format. |
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123 + The tool accepts annotation and operon files in: |
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124 + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon") |
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125 + the format used by NCBI for genes ("Summary (text)"); |
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126 + four tab-separated columns: sequence name, gene/operon id, start position, end position |
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127 |
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128 - Output: |
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129 + An assessment summary in plain text format |
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130 + An assessment summary in tabulation separated values format |
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131 + An assessment summary in LateX format |
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132 + An assessment summary in HTML format |
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133 + An HTML view of contig sizes wit Icarus |
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134 |
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135 |
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136 ]]> |
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137 </help> |
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138 |
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139 <citations> |
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140 <citation type="bibtex">@ARTICLE{a1, |
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141 author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler}, |
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142 title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075} |
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143 }</citation> |
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144 <citation type="bibtex">@misc{quast41, |
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145 title = {{Quast} v4.1}, |
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146 howpublished = {http://bioinf.spbau.ru/quast}, |
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147 note = {Released May 2016}} |
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148 }</citation> |
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149 </citations> |
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150 </tool> |