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annotate gemini_fusions.xml @ 0:c974176a17cc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:52:33 -0500
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children b737121efb78
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c974176a17cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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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[
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13 gemini @BINARY@
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c974176a17cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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15 #if $annotation_databases:
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16 --annotation-dir "${ annotation_databases.fields.path }"
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17 #end if
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18
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19 $in_cosmic_census
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21 #if float($min_quality) >= 0:
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22 --min-qual $min_quality
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23 #end if
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25 #if str($evidence_type):
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26 --evidence_type $evidence_type
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27 #end if
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29 "${ infile }" | tr -s ' ' '\t'
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30 > "${ outfile }"
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31 ]]>
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32 </command>
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33 <inputs>
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c974176a17cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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35 <expand macro="infile" />
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36 <expand macro="annotation_dir" />
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38 <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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40 <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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42 <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
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43 <option value="" selected="True">select one (optional)</option>
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44 <option value="PE">PE</option>
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45 <option value="SR">SR</option>
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46 <option value="PE,SR">PE,SR</option>
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47 </param>
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48
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49 </inputs>
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50 <outputs>
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51 <data name="outfile" format="tabular" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <!-- Like in set_somatic this example is nonsensical because otherwise
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56 the testdata would be too big. The resulting output should be empty.-->
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57 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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58 <output name="outfile" file="gemini_fusions_result.tabular" />
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59 </test>
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60 </tests>
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61 <help>
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62 <![CDATA[
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63 **What it does**
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64
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65 Identifies somatic fusion genes from a GEMINI database.
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66 ]]>
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67 </help>
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68 <expand macro="citations"/>
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69 </tool>