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annotate gemini_fusions.xml @ 1:37f9901b674d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 7867095d83e5d0e0f923de7e9720d59df0034817
author iuc
date Tue, 22 Mar 2016 21:42:02 -0400
parents 8295781a3c27
children b35fd707c586
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8295781a3c27 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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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[
8295781a3c27 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12
1
37f9901b674d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 7867095d83e5d0e0f923de7e9720d59df0034817
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13 gemini
0
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14 #if $annotation_databases:
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15 --annotation-dir "${ annotation_databases.fields.path }"
8295781a3c27 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 #end if
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17 @BINARY@
0
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18 $in_cosmic_census
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20 #if float($min_quality) >= 0:
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21 --min-qual $min_quality
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22 #end if
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24 #if str($evidence_type):
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25 --evidence_type $evidence_type
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26 #end if
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28 "${ infile }" | tr -s ' ' '\t'
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29 > "${ outfile }"
8295781a3c27 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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30 ]]>
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31 </command>
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32 <inputs>
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8295781a3c27 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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34 <expand macro="infile" />
8295781a3c27 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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35 <expand macro="annotation_dir" />
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37 <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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38
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39 <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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41 <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
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42 <option value="" selected="True">select one (optional)</option>
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43 <option value="PE">PE</option>
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44 <option value="SR">SR</option>
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45 <option value="PE,SR">PE,SR</option>
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46 </param>
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47
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48 </inputs>
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49 <outputs>
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50 <data name="outfile" format="tabular" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <!-- Like in set_somatic this example is nonsensical because otherwise
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55 the testdata would be too big. The resulting output should be empty.-->
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56 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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57 <output name="outfile" file="gemini_fusions_result.tabular" />
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62 **What it does**
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63
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64 Identifies somatic fusion genes from a GEMINI database.
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65 ]]>
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66 </help>
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67 <expand macro="citations"/>
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68 </tool>