Mercurial > repos > iuc > sansa_annotate

annotate annotate.xml @ 2:30079fa4e2fd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit f62fcf6b6a22e6514a5e455ab0e9b42ad712c1be"
author iuc
date Sat, 17 Apr 2021 08:49:25 +0000
parents e3862632706d
children b1ca9fce4749
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1 <?xml version="1.0"?>
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2 <tool id="sansa_annotate" name="sansa annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
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3 <description>structural variants</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
1
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7 <expand macro="edam_topics"/>
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8 <expand macro="edam_operations"/>
0
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9 <expand macro="requirements"/>
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10 <expand macro="version_command"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## initialize
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13 ## file format gtf.gz is required
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14 #if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg'
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15 gzip -c '$type_cond.fg.gtf' > 'db.gtf.gz' &&
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16 #end if
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17
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18 ## run
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19 sansa annotate
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20 ## sv annotation options
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21 #if $type_cond.type_sel == 's' or $type_cond.type_sel == 'sfg'
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22 --db '$type_cond.s.db'
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23 --bpoffset $type_cond.s.bpoffset
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24 --ratio $type_cond.s.ratio
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25 --strategy '$type_cond.s.strategy'
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26 $type_cond.s.notype
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27 $type_cond.s.nomatch
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28 #end if
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29 ## feature and gene annotation options
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30 #if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg'
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31 --gtf 'db.gtf.gz'
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32 --id '$type_cond.fg.id'
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33 --feature '$type_cond.fg.feature'
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34 --distance $type_cond.fg.distance
2
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35 $type_cond.fg.contained
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36 #end if
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37 ## input
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38 '$input'
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39
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40 ## postprocessing
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41 2>&1 | tee -a '$out_log'
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42 ]]></command>
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43 <inputs>
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44 <param name="input" type="data" format="vcf" label="Select input file"/>
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45 <conditional name="type_cond">
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46 <param name="type_sel" type="select" label="Select annotation mode(s)">
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47 <option value="s" selected="true">SV</option>
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48 <option value="fg">Feature/Gene</option>
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49 <option value="sfg">SV and Feature/Gene</option>
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50 </param>
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51 <when value="s">
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52 <expand macro="s"/>
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53 </when>
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54 <when value="fg">
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55 <expand macro="fg"/>
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56 </when>
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57 <when value="sfg">
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58 <expand macro="s"/>
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59 <expand macro="fg"/>
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60 </when>
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61 </conditional>
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62 <section name="oo" title="Output options" expanded="true">
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63 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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64 <option value="anno" selected="true">Annotation</option>
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65 <option value="log">Log</option>
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66 <option value="query">Query SV</option>
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67 </param>
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68 </section>
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69 </inputs>
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70 <outputs>
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71 <data name="out_anno" format="bcf" from_work_dir="anno.bcf" label="${tool.name} on ${on_string}: Annotation">
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72 <filter>'anno' in oo['out']</filter>
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73 </data>
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74 <data name="out_query" format="tabular.gz" from_work_dir="query.tsv.gz" label="${tool.name} on ${on_string}: Query SV">
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75 <filter>'query' in oo['out']</filter>
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76 </data>
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77 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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78 <filter>'log' in oo['out']</filter>
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79 </data>
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80 </outputs>
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81 <tests>
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82 <!-- #1 s, default -->
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83 <test expect_num_outputs="3">
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84 <param name="input" value="input.vcf"/>
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85 <conditional name="type_cond">
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86 <param name="type_sel" value="s"/>
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87 <section name="s">
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88 <param name="db" value="db.vcf"/>
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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 changeset
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 changeset
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 changeset
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 changeset
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:
diff changeset
169 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
170 </test>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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 changeset
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 changeset
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 changeset
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 changeset
182 </section>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
183 </conditional>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
184 <section name="oo">
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
186 </section>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
188 <assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
190 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
195 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
196 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
198 <assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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 changeset
208 <section name="s">
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
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 changeset
213 </section>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
219 <assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
221 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
226 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
227 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
232 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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 changeset
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 changeset
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 changeset
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 changeset
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 changeset
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"
iuc
parents:
diff changeset
255 <section name="oo">
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
256 <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
257 </section>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
258 <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
259 <assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
260 <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
261 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
262 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
263 <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
264 <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
265 <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 changeset
266 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
267 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
268 <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
269 <assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
270 <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
271 </assert_contents>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
272 </output>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
273 </test>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
274 </tests>
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
275 <help><![CDATA[
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
276 .. class:: infomark
fb00426402b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
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
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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>`_
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287
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288 **Output**
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289
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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>