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annotate describe_samples.xml @ 5:ad1b16addfa3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author iuc
date Mon, 28 Aug 2017 16:55:02 -0400
parents 5bb8e7dcc404
children fee2817c25a8
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5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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1 <?xml version="1.0"?>
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2 <tool id="describe_samples" name="Describe samples" version="@WRAPPER_VERSION@.0">
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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 <command detect_errors="aggressive"><![CDATA[
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8 cp $sample_list $output
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="sample_list"><![CDATA[#for $sample in $samples:
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12 $sample.condition $sample.name
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13 #end for]]></configfile>
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14 </configfiles>
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15 <inputs>
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16 <repeat name="samples" title="Samples">
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17 <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" optional="False" />
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18 <param name="condition" type="text" label="Condition" help="e.g. ConditionA" optional="False" />
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19 </repeat>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="output"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <repeat name="samples">
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27 <param name="condition" value="ConditionA" />
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28 <param name="name" value="CondA_replicate1" />
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29 </repeat>
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30 <repeat name="samples">
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31 <param name="condition" value="ConditionA" />
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32 <param name="name" value="CondA_replicate2" />
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33 </repeat>
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34 <repeat name="samples">
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35 <param name="condition" value="ConditionB" />
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36 <param name="name" value="CondB_replicate1" />
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37 </repeat>
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38 <repeat name="samples">
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39 <param name="condition" value="ConditionB" />
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40 <param name="name" value="CondB_replicate2" />
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41 </repeat>
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42 <output name="output" file="samples.tsv"/>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 This tools allows to describe your samples and replicates, producing a tabular file looking like this:
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47
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48 =========== ================
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49 ConditionA CondA_replicate1
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50 ----------- ----------------
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51 ConditionA CondA_replicate2
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52 ----------- ----------------
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53 ConditionB CondB_replicate1
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54 ----------- ----------------
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55 ConditionB CondB_replicate2
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56 ----------- ----------------
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57 ConditionC CondC_replicate1
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58 ----------- ----------------
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59 ConditionC CondC_replicate2
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60 ----------- ----------------
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61 ConditionC CondC_replicate3
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62 =========== ================
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63
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64 IThe output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'.
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65 The names in column 2 must match the names given to the datasets in your history.
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66 ]]></help>
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67 <expand macro="citation"/>
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68 </tool>