Mercurial > repos > iuc > sansa_annotate
annotate annotate.xml @ 2:30079fa4e2fd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit f62fcf6b6a22e6514a5e455ab0e9b42ad712c1be"
author | iuc |
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date | Sat, 17 Apr 2021 08:49:25 +0000 |
parents | e3862632706d |
children | b1ca9fce4749 |
rev | line source |
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0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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1 <?xml version="1.0"?> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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2 <tool id="sansa_annotate" name="sansa annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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3 <description>structural variants</description> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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4 <macros> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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5 <import>macros.xml</import> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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6 </macros> |
1
e3862632706d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents:
0
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7 <expand macro="edam_topics"/> |
e3862632706d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents:
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8 <expand macro="edam_operations"/> |
0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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9 <expand macro="requirements"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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10 <expand macro="version_command"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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11 <command detect_errors="exit_code"><![CDATA[ |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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12 ## initialize |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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13 ## file format gtf.gz is required |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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14 #if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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15 gzip -c '$type_cond.fg.gtf' > 'db.gtf.gz' && |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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16 #end if |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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17 |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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18 ## run |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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19 sansa annotate |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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20 ## sv annotation options |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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21 #if $type_cond.type_sel == 's' or $type_cond.type_sel == 'sfg' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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22 --db '$type_cond.s.db' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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23 --bpoffset $type_cond.s.bpoffset |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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24 --ratio $type_cond.s.ratio |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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25 --strategy '$type_cond.s.strategy' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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26 $type_cond.s.notype |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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27 $type_cond.s.nomatch |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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28 #end if |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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29 ## feature and gene annotation options |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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30 #if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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31 --gtf 'db.gtf.gz' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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32 --id '$type_cond.fg.id' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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33 --feature '$type_cond.fg.feature' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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34 --distance $type_cond.fg.distance |
2
30079fa4e2fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit f62fcf6b6a22e6514a5e455ab0e9b42ad712c1be"
iuc
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35 $type_cond.fg.contained |
0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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36 #end if |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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37 ## input |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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38 '$input' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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39 |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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40 ## postprocessing |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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41 2>&1 | tee -a '$out_log' |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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42 ]]></command> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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43 <inputs> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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44 <param name="input" type="data" format="vcf" label="Select input file"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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45 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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46 <param name="type_sel" type="select" label="Select annotation mode(s)"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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47 <option value="s" selected="true">SV</option> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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48 <option value="fg">Feature/Gene</option> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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49 <option value="sfg">SV and Feature/Gene</option> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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50 </param> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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51 <when value="s"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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52 <expand macro="s"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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53 </when> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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54 <when value="fg"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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55 <expand macro="fg"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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56 </when> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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57 <when value="sfg"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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58 <expand macro="s"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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59 <expand macro="fg"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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60 </when> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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61 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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62 <section name="oo" title="Output options" expanded="true"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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63 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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64 <option value="anno" selected="true">Annotation</option> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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65 <option value="log">Log</option> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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66 <option value="query">Query SV</option> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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67 </param> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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68 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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69 </inputs> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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70 <outputs> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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71 <data name="out_anno" format="bcf" from_work_dir="anno.bcf" label="${tool.name} on ${on_string}: Annotation"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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72 <filter>'anno' in oo['out']</filter> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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73 </data> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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74 <data name="out_query" format="tabular.gz" from_work_dir="query.tsv.gz" label="${tool.name} on ${on_string}: Query SV"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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75 <filter>'query' in oo['out']</filter> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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76 </data> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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77 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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78 <filter>'log' in oo['out']</filter> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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79 </data> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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80 </outputs> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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81 <tests> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
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82 <!-- #1 s, default --> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
83 <test expect_num_outputs="3"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
84 <param name="input" value="input.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
85 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
86 <param name="type_sel" value="s"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
87 <section name="s"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
88 <param name="db" value="db.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
89 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
90 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
91 <section name="oo"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
92 <param name="out" value="anno,log,query"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
93 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
94 <output name="out_anno"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
95 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
96 <has_size value="57072"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
97 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
98 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
99 <output name="out_query"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
100 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
101 <has_size value="91"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
102 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
103 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
104 <output name="out_log"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
105 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
106 <has_text_matching expression=".+Done.+"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
107 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
108 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
109 </test> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
110 <!-- #2 s, custom --> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
111 <test expect_num_outputs="3"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
112 <param name="input" value="input.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
113 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
114 <param name="type_sel" value="s"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
115 <section name="s"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
116 <param name="db" value="db.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
117 <param name="bpoffset" value="51"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
118 <param name="ratio" value="0.79"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
119 <param name="strategy" value="all"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
120 <param name="notype" value="true"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
121 <param name="nomatch" value="true"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
122 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
123 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
124 <section name="oo"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
125 <param name="out" value="anno,log,query"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
126 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
127 <output name="out_anno"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
128 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
129 <has_size value="57072"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
130 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
131 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
132 <output name="out_query"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
133 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
134 <has_size value="91"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
135 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
136 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
137 <output name="out_log"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
138 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
139 <has_text_matching expression=".+Done.+"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
140 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
141 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
142 </test> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
143 <!-- #3 fg, default --> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
144 <test expect_num_outputs="3"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
145 <param name="input" value="input.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
146 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
147 <param name="type_sel" value="fg"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
148 <section name="fg"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
149 <param name="gtf" value="db.gtf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
150 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
151 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
152 <section name="oo"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
153 <param name="out" value="anno,log,query"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
154 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
155 <output name="out_anno"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
156 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
157 <has_size value="2408"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
158 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
159 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
160 <output name="out_query"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
161 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
162 <has_size value="91"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
163 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
164 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
165 <output name="out_log"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
166 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
167 <has_text_matching expression=".+Done.+"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
168 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
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169 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
170 </test> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
171 <!-- #4 fg, custom --> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
172 <test expect_num_outputs="3"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
173 <param name="input" value="input.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
174 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
175 <param name="type_sel" value="fg"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
176 <section name="fg"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
177 <param name="gtf" value="db.gtf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
178 <param name="id" value="gene_id"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
179 <param name="feature" value="exon"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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180 <param name="distance" value="1001"/> |
1
e3862632706d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents:
0
diff
changeset
|
181 <param name="contained" value="true"/> |
0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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182 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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183 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
184 <section name="oo"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
185 <param name="out" value="anno,log,query"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
186 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
187 <output name="out_anno"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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188 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
189 <has_size value="2408"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
190 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
191 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
192 <output name="out_query"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
193 <assert_contents> |
2
30079fa4e2fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit f62fcf6b6a22e6514a5e455ab0e9b42ad712c1be"
iuc
parents:
1
diff
changeset
|
194 <has_size value="101"/> |
0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
195 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
196 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
197 <output name="out_log"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
198 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
199 <has_text_matching expression=".+Done.+"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
200 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
201 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
202 </test> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
203 <!-- #5 sfg, default --> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
204 <test expect_num_outputs="3"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
205 <param name="input" value="input.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
206 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
207 <param name="type_sel" value="sfg"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
208 <section name="s"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
209 <param name="db" value="db.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
210 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
211 <section name="fg"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
212 <param name="gtf" value="db.gtf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
213 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
214 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
215 <section name="oo"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
216 <param name="out" value="anno,log,query"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
217 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
218 <output name="out_anno"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
219 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
220 <has_size value="57072"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
221 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
222 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
223 <output name="out_query"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
224 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
225 <has_size value="91"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
226 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
227 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
228 <output name="out_log"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
229 <assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
230 <has_text_matching expression=".+Done.+"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
231 </assert_contents> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
232 </output> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
233 </test> |
1
e3862632706d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents:
0
diff
changeset
|
234 <!-- #6 sfg, custom --> |
0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
235 <test expect_num_outputs="3"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
236 <param name="input" value="input.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
237 <conditional name="type_cond"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
238 <param name="type_sel" value="sfg"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
239 <section name="s"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
240 <param name="db" value="db.vcf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
241 <param name="bpoffset" value="51"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
242 <param name="ratio" value="0.79"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
243 <param name="strategy" value="all"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
244 <param name="notype" value="true"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
245 <param name="nomatch" value="true"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
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|
246 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
247 <section name="fg"> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
248 <param name="gtf" value="db.gtf"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
249 <param name="id" value="gene_id"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
250 <param name="feature" value="exon"/> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
251 <param name="distance" value="1001"/> |
1
e3862632706d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents:
0
diff
changeset
|
252 <param name="contained" value="true"/> |
0
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
253 </section> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff
changeset
|
254 </conditional> |
fb00426402b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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255 <section name="oo"> |
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256 <param name="out" value="anno,log,query"/> |
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257 </section> |
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258 <output name="out_anno"> |
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259 <assert_contents> |
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260 <has_size value="57072"/> |
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261 </assert_contents> |
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262 </output> |
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263 <output name="out_query"> |
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264 <assert_contents> |
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265 <has_size value="101"/> |
0
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266 </assert_contents> |
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267 </output> |
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268 <output name="out_log"> |
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269 <assert_contents> |
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270 <has_text_matching expression=".+Done.+"/> |
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271 </assert_contents> |
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272 </output> |
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273 </test> |
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274 </tests> |
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275 <help><![CDATA[ |
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276 .. class:: infomark |
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277 |
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278 **What it does** |
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279 |
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280 Sansa *annotate* is a structural variant (SV) annotation tool. |
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281 |
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282 **Input** |
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283 |
1
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284 - Sample (VCF) |
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285 - Gene annotation (GTF/GFF2/GFF3) |
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286 - Annotation database, e.g. `gnomAD-SV <https://gnomad.broadinstitute.org/>`_ or `1000 Genomes phase 3 <https://www.internationalgenome.org/phase-3-structural-variant-dataset>`_ |
0
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287 |
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288 **Output** |
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289 |
1
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290 - Anno (BCF) with annotation SVs augmented by a unique ID (INFO/ANNOID) |
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291 - Query (TABULAR.GZ) with query SVs matched to annotation IDs |
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292 |
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293 .. class:: infomark |
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294 |
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295 **References** |
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296 |
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297 More information are available on `GitHub <https://github.com/dellytools/sansa>`_. |
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298 ]]></help> |
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299 <citations> |
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300 <citation type="doi">10.1093/bioinformatics/bts378</citation> |
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301 </citations> |
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302 </tool> |