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annotate gemini_fusions.xml @ 3:142dbbe778c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:27:59 -0500
parents b737121efb78
children b57a5db5688d
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
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2 <description>Identify somatic fusion genes from a GEMINI database</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">fusions</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
1
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12 @PROVIDE_ANNO_DATA@
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14 gemini
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15 @BINARY@
0
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16 $in_cosmic_census
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18 #if float($min_quality) >= 0:
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19 --min-qual $min_quality
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20 #end if
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22 #if str($evidence_type):
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23 --evidence_type $evidence_type
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24 #end if
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26 "${ infile }" | tr -s ' ' '\t'
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27 > "${ outfile }"
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28 ]]>
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29 </command>
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30 <inputs>
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32 <expand macro="infile" />
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33 <expand macro="annotation_dir" />
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35 <param argument="--in_cosmic_census" type="boolean" truevalue="--in_cosmic_census" falsevalue="" checked="False" label="One or both genes in fusion is in COSMIC cancer census" />
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37 <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min_qual)"/>
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39 <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
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40 <option value="" selected="True">select one (optional)</option>
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41 <option value="PE">PE</option>
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42 <option value="SR">SR</option>
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43 <option value="PE,SR">PE,SR</option>
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44 </param>
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45
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46 </inputs>
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47 <outputs>
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48 <data name="outfile" format="tabular" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <!-- Like in set_somatic this example is nonsensical because otherwise
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53 the testdata would be too big. The resulting output should be empty.-->
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54 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
0
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55 <output name="outfile" file="gemini_fusions_result.tabular" />
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56 </test>
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57 </tests>
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58 <help>
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59 <![CDATA[
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60 **What it does**
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61
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62 Identifies somatic fusion genes from a GEMINI database.
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63 ]]>
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64 </help>
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65 <expand macro="citations"/>
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66 </tool>