Mercurial > repos > iuc > sansa_annotate

annotate annotate.xml @ 1:b4b8e88c6ff9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
author iuc
date Fri, 16 Apr 2021 21:31:21 +0000
parents 608c3eefface
children c3877d3a230e
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608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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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 $type_cond.fg.distance
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35 #end if
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36 ## input
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37 '$input'
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38
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39 ## postprocessing
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40 2>&1 | tee -a '$out_log'
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41 ]]></command>
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42 <inputs>
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43 <param name="input" type="data" format="vcf" label="Select input file"/>
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44 <conditional name="type_cond">
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45 <param name="type_sel" type="select" label="Select annotation mode(s)">
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46 <option value="s" selected="true">SV</option>
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47 <option value="fg">Feature/Gene</option>
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48 <option value="sfg">SV and Feature/Gene</option>
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49 </param>
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50 <when value="s">
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51 <expand macro="s"/>
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52 </when>
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53 <when value="fg">
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54 <expand macro="fg"/>
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55 </when>
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56 <when value="sfg">
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57 <expand macro="s"/>
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58 <expand macro="fg"/>
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59 </when>
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60 </conditional>
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61 <section name="oo" title="Output options" expanded="true">
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62 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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63 <option value="anno" selected="true">Annotation</option>
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64 <option value="log">Log</option>
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65 <option value="query">Query SV</option>
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66 </param>
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67 </section>
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68 </inputs>
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69 <outputs>
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70 <data name="out_anno" format="bcf" from_work_dir="anno.bcf" label="${tool.name} on ${on_string}: Annotation">
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71 <filter>'anno' in oo['out']</filter>
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72 </data>
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73 <data name="out_query" format="tabular.gz" from_work_dir="query.tsv.gz" label="${tool.name} on ${on_string}: Query SV">
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74 <filter>'query' in oo['out']</filter>
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75 </data>
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76 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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77 <filter>'log' in oo['out']</filter>
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78 </data>
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79 </outputs>
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80 <tests>
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81 <!-- #1 s, default -->
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82 <test expect_num_outputs="3">
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83 <param name="input" value="input.vcf"/>
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84 <conditional name="type_cond">
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85 <param name="type_sel" value="s"/>
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86 <section name="s">
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87 <param name="db" value="db.vcf"/>
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88 </section>
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89 </conditional>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
90 <section name="oo">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
91 <param name="out" value="anno,log,query"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
92 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
93 <output name="out_anno">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
94 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
95 <has_size value="57072"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
96 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
97 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
98 <output name="out_query">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
99 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
100 <has_size value="91"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
101 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
102 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
103 <output name="out_log">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
104 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
105 <has_text_matching expression=".+Done.+"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
106 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
107 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
108 </test>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
109 <!-- #2 s, custom -->
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
110 <test expect_num_outputs="3">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
111 <param name="input" value="input.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
112 <conditional name="type_cond">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
113 <param name="type_sel" value="s"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
114 <section name="s">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
115 <param name="db" value="db.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
116 <param name="bpoffset" value="51"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
117 <param name="ratio" value="0.79"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
118 <param name="strategy" value="all"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
119 <param name="notype" value="true"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
120 <param name="nomatch" value="true"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
121 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
122 </conditional>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
123 <section name="oo">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
124 <param name="out" value="anno,log,query"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
125 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
126 <output name="out_anno">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
127 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
128 <has_size value="57072"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
129 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
130 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
131 <output name="out_query">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
132 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
133 <has_size value="91"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
134 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
135 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
136 <output name="out_log">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
137 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
138 <has_text_matching expression=".+Done.+"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
139 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
140 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
141 </test>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
142 <!-- #3 fg, default -->
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
143 <test expect_num_outputs="3">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
144 <param name="input" value="input.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
145 <conditional name="type_cond">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
146 <param name="type_sel" value="fg"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
147 <section name="fg">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
148 <param name="gtf" value="db.gtf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
149 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
150 </conditional>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
151 <section name="oo">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
152 <param name="out" value="anno,log,query"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
153 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
154 <output name="out_anno">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
155 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
156 <has_size value="2408"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
157 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
158 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
159 <output name="out_query">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
160 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
161 <has_size value="91"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
162 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
163 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
164 <output name="out_log">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
165 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
166 <has_text_matching expression=".+Done.+"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
167 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
168 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
169 </test>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
170 <!-- #4 fg, custom -->
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
171 <test expect_num_outputs="3">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
172 <param name="input" value="input.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
173 <conditional name="type_cond">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
174 <param name="type_sel" value="fg"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
175 <section name="fg">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
176 <param name="gtf" value="db.gtf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
177 <param name="id" value="gene_id"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
178 <param name="feature" value="exon"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
179 <param name="distance" value="1001"/>
1
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents: 0
diff changeset
180 <param name="contained" value="true"/>
0
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
181 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
182 </conditional>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
183 <section name="oo">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
184 <param name="out" value="anno,log,query"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
185 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
186 <output name="out_anno">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
187 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
188 <has_size value="2408"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
189 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
190 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
191 <output name="out_query">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
192 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
193 <has_size value="91"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
194 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
195 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
196 <output name="out_log">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
197 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
198 <has_text_matching expression=".+Done.+"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
199 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
200 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
201 </test>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
202 <!-- #5 sfg, default -->
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
203 <test expect_num_outputs="3">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
204 <param name="input" value="input.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
205 <conditional name="type_cond">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
206 <param name="type_sel" value="sfg"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
207 <section name="s">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
208 <param name="db" value="db.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
209 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
210 <section name="fg">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
211 <param name="gtf" value="db.gtf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
212 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
213 </conditional>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
214 <section name="oo">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
215 <param name="out" value="anno,log,query"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
216 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
217 <output name="out_anno">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
218 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
219 <has_size value="57072"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
220 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
221 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
222 <output name="out_query">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
223 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
224 <has_size value="91"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
225 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
226 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
227 <output name="out_log">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
228 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
229 <has_text_matching expression=".+Done.+"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
230 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
231 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
232 </test>
1
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents: 0
diff changeset
233 <!-- #6 sfg, custom -->
0
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
234 <test expect_num_outputs="3">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
235 <param name="input" value="input.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
236 <conditional name="type_cond">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
237 <param name="type_sel" value="sfg"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
238 <section name="s">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
239 <param name="db" value="db.vcf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
240 <param name="bpoffset" value="51"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
241 <param name="ratio" value="0.79"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
242 <param name="strategy" value="all"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
243 <param name="notype" value="true"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
244 <param name="nomatch" value="true"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
245 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
246 <section name="fg">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
247 <param name="gtf" value="db.gtf"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
248 <param name="id" value="gene_id"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
249 <param name="feature" value="exon"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
250 <param name="distance" value="1001"/>
1
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
iuc
parents: 0
diff changeset
251 <param name="contained" value="true"/>
0
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
252 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
253 </conditional>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
254 <section name="oo">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
255 <param name="out" value="anno,log,query"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
256 </section>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
257 <output name="out_anno">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
258 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
259 <has_size value="57072"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
260 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
261 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
262 <output name="out_query">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
263 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
264 <has_size value="91"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
265 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
266 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
267 <output name="out_log">
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
268 <assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
269 <has_text_matching expression=".+Done.+"/>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
270 </assert_contents>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
271 </output>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
272 </test>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
273 </tests>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
274 <help><![CDATA[
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
275 .. class:: infomark
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
276
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
iuc
parents:
diff changeset
277 **What it does**
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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278
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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279 Sansa *annotate* is a structural variant (SV) annotation tool.
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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280
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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281 **Input**
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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282
1
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283 - Sample (VCF)
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
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284 - Gene annotation (GTF/GFF2/GFF3)
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
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285 - 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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608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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286
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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287 **Output**
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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288
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289 - Anno (BCF) with annotation SVs augmented by a unique ID (INFO/ANNOID)
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
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290 - Query (TABULAR.GZ) with query SVs matched to annotation IDs
0
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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291
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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292 .. class:: infomark
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293
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294 **References**
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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295
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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296 More information are available on `GitHub <https://github.com/dellytools/sansa>`_.
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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297 ]]></help>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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298 <citations>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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299 <citation type="doi">10.1093/bioinformatics/bts378</citation>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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300 </citations>
608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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301 </tool>