Mercurial > repos > iuc > gemini_fusions

annotate gemini_fusions.xml @ 8:c00dcd1455a0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:33:52 +0000
parents 6e3d2bd01a96
children
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Identify somatic fusion genes from a GEMINI database</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">fusions</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 @PROVIDE_ANNO_DATA@
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15 gemini
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16 @BINARY@
0
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17 $in_cosmic_census
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19 #if float($min_quality) >= 0:
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20 --min-qual $min_quality
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21 #end if
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23 #if str($evidence_type):
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24 --evidence_type $evidence_type
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25 #end if
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26
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27 '$infile' | tr -s ' ' '\t'
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28 > '$outfile'
0
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29 ]]>
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30 </command>
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31 <inputs>
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33 <expand macro="infile" />
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34 <expand macro="annotation_dir" />
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36 <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 <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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40 <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
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41 <option value="" selected="True">select one (optional)</option>
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42 <option value="PE">PE</option>
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43 <option value="SR">SR</option>
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44 <option value="PE,SR">PE,SR</option>
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45 </param>
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46
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47 </inputs>
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48 <outputs>
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49 <data name="outfile" format="tabular" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <!-- Like in set_somatic this example is nonsensical because otherwise
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54 the testdata would be too big. The resulting output should be empty.-->
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55 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
0
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56 <output name="outfile" file="gemini_fusions_result.tabular" />
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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61 **What it does**
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62
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63 Identifies somatic fusion genes from a GEMINI database.
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64 ]]>
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65 </help>
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66 <expand macro="citations"/>
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67 </tool>