Mercurial > repos > iuc > gemini_amend

annotate gemini_amend.xml @ 3:caaf7e559f4d 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 12:29:29 -0500
parents c84586bd8d34
children 939636ef501b
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5845a899e87d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Amend an already loaded 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@">amend</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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12 cp "${ infile }" "${ outfile }" &&
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092ce14766b5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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14 gemini @BINARY@
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15 $clear
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16 --sample "${ ped }"
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18 "${ outfile }"
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19 ]]>
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20 </command>
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21 <inputs>
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23 <expand macro="infile" />
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24 <param name="ped" type="data" format="tabular" optional="True" label="Additional sample information file in PED+ format" help="(--sample)" />
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25 <param argument="--clear" type="boolean" truevalue="--clear" falsevalue="" checked="False" label="Set all values to None before loading" help="Makes it possible to delete values. Otherwise the old ones are kept"/>
092ce14766b5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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27 </inputs>
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28 <outputs>
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29 <data name="outfile" format="gemini.sqlite" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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caaf7e559f4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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34 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
caaf7e559f4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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35 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
0
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
092ce14766b5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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40 **What it does**
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092ce14766b5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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42 Gemini amend adds information about the samples via PED file.
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44 If you have a sample table in a Gemini db that looks like this::
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46 sample_id family_id name paternal_id maternal_id sex phenotype hair_color
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47 1 1 M10475 0 0 1 1 brown
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48 2 1 M10478 M10475 M10500 2 2 blonde
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49 3 1 M10500 0 0 2 2 purple
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51 and you want the change the haircolor of sample 3. And also add some information about the preferred hobbies of some samples.
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52
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53 You could specify the following PED file. ::
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54
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55 #family_id name paternal_id maternal_id sex phenotype hair_color hobby
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56 1 M10475 None None 1 1 brown fishing
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57 1 M10478 M10475 M10500 2 2 red biking
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58 1 M10500 None None 2 2 purple
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59
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60 this results in::
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61
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62 sample_id family_id name paternal_id maternal_id sex phenotype hair_color hobby
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63 1 1 M10475 0 0 1 1 brown fishing
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64 2 1 M10478 M10475 M10500 2 2 red biking
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65 3 1 M10500 0 0 2 2 purple .
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66
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67 ]]>
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68 </help>
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69 <expand macro="citations"/>
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70 </tool>