Mercurial > repos > iuc > gemini_amend

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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 15:29:47 +0000
parents bff8fad3fb69
children
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bff8fad3fb69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Amend an already loaded 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>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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6 <token name="@BINARY@">amend</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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10 <expand macro="version_command" />
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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11 <command>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12 <![CDATA[
5
bff8fad3fb69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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13 cp '$infile' '$outfile' &&
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ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 gemini @BINARY@
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 $clear
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17 --sample '$ped'
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18
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19 '$outfile'
0
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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20 ]]>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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21 </command>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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22 <inputs>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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24 <expand macro="infile" />
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25 <param name="ped" type="data" format="tabular" optional="True" label="Additional sample information file in PED+ format" help="(--sample)" />
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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26 <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"/>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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28 </inputs>
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29 <outputs>
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30 <data name="outfile" format="gemini.sqlite" />
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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31 </outputs>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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32 <tests>
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33 <test>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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34 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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35 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
a02cd62adb70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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36 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
0
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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37 </test>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38 </tests>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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39 <help>
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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40 <![CDATA[
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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41 **What it does**
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ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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43 Gemini amend adds information about the samples via PED file.
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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44
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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45 If you have a sample table in a Gemini db that looks like this::
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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46
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47 sample_id family_id name paternal_id maternal_id sex phenotype hair_color
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48 1 1 M10475 0 0 1 1 brown
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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49 2 1 M10478 M10475 M10500 2 2 blonde
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50 3 1 M10500 0 0 2 2 purple
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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51
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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52 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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53
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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54 You could specify the following PED file. ::
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55
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56 #family_id name paternal_id maternal_id sex phenotype hair_color hobby
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57 1 M10475 None None 1 1 brown fishing
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58 1 M10478 M10475 M10500 2 2 red biking
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59 1 M10500 None None 2 2 purple
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60
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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61 this results in::
ccd8fdcf82d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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62
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63 sample_id family_id name paternal_id maternal_id sex phenotype hair_color hobby
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64 1 1 M10475 0 0 1 1 brown fishing
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65 2 1 M10478 M10475 M10500 2 2 red biking
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66 3 1 M10500 0 0 2 2 purple .
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67
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68 ]]>
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69 </help>
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70 <expand macro="citations"/>
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71 </tool>