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annotate describe_samples.xml @ 17:e3b16fd7dd08 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1b2ce625fad2514549bf2a675c26517c3d46ed81"
author iuc
date Sun, 19 Dec 2021 16:24:50 +0000
parents 0f294e370b95
children 57f477b57c35
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1 <?xml version="1.0"?>
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2 <tool id="describe_samples" name="Describe samples" version="@WRAPPER_VERSION@">
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3 <description>and replicates</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 cp $sample_list $output
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="sample_list"><![CDATA[#for $sample in $samples:
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13 $sample.condition $sample.name
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14 #end for]]></configfile>
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15 </configfiles>
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16 <inputs>
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17 <repeat name="samples" title="Samples">
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18 <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" optional="False" />
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19 <param name="condition" type="text" label="Condition" help="e.g. ConditionA" optional="False" />
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20 </repeat>
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <repeat name="samples">
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28 <param name="condition" value="ConditionA" />
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29 <param name="name" value="CondA_replicate1" />
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30 </repeat>
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31 <repeat name="samples">
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32 <param name="condition" value="ConditionA" />
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33 <param name="name" value="CondA_replicate2" />
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34 </repeat>
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35 <repeat name="samples">
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36 <param name="condition" value="ConditionB" />
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37 <param name="name" value="CondB_replicate1" />
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38 </repeat>
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39 <repeat name="samples">
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40 <param name="condition" value="ConditionB" />
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41 <param name="name" value="CondB_replicate2" />
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42 </repeat>
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43 <output name="output" file="samples.tsv"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 This tools allows to describe your samples and replicates, producing a tabular file looking like this:
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48
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49 =========== ================
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50 ConditionA CondA_replicate1
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51 ----------- ----------------
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52 ConditionA CondA_replicate2
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53 ----------- ----------------
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54 ConditionB CondB_replicate1
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55 ----------- ----------------
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56 ConditionB CondB_replicate2
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57 ----------- ----------------
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58 ConditionC CondC_replicate1
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59 ----------- ----------------
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60 ConditionC CondC_replicate2
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61 ----------- ----------------
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62 ConditionC CondC_replicate3
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63 =========== ================
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64
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65 IThe output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'.
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66 The names in column 2 must match the names given to the datasets in your history.
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67 ]]></help>
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68 <expand macro="citation"/>
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69 </tool>