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