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comparison describe_samples.xml @ 0:5bb8e7dcc404 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
author iuc
date Fri, 18 Nov 2016 06:07:54 -0500
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1 <?xml version="1.0"?>
2 <tool id="describe_samples" name="Describe samples" version="@WRAPPER_VERSION@.0">
3 <description>and replicates</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <command detect_errors="aggressive"><![CDATA[
8 cp $sample_list $output
9 ]]></command>
10 <configfiles>
11 <configfile name="sample_list"><![CDATA[#for $sample in $samples:
12 $sample.condition $sample.name
13 #end for]]></configfile>
14 </configfiles>
15 <inputs>
16 <repeat name="samples" title="Samples">
17 <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" optional="False" />
18 <param name="condition" type="text" label="Condition" help="e.g. ConditionA" optional="False" />
19 </repeat>
20 </inputs>
21 <outputs>
22 <data format="tabular" name="output"/>
23 </outputs>
24 <tests>
25 <test>
26 <repeat name="samples">
27 <param name="condition" value="ConditionA" />
28 <param name="name" value="CondA_replicate1" />
29 </repeat>
30 <repeat name="samples">
31 <param name="condition" value="ConditionA" />
32 <param name="name" value="CondA_replicate2" />
33 </repeat>
34 <repeat name="samples">
35 <param name="condition" value="ConditionB" />
36 <param name="name" value="CondB_replicate1" />
37 </repeat>
38 <repeat name="samples">
39 <param name="condition" value="ConditionB" />
40 <param name="name" value="CondB_replicate2" />
41 </repeat>
42 <output name="output" file="samples.tsv"/>
43 </test>
44 </tests>
45 <help><![CDATA[
46 This tools allows to describe your samples and replicates, producing a tabular file looking like this:
47
48 =========== ================
49 ConditionA CondA_replicate1
50 ----------- ----------------
51 ConditionA CondA_replicate2
52 ----------- ----------------
53 ConditionB CondB_replicate1
54 ----------- ----------------
55 ConditionB CondB_replicate2
56 ----------- ----------------
57 ConditionC CondC_replicate1
58 ----------- ----------------
59 ConditionC CondC_replicate2
60 ----------- ----------------
61 ConditionC CondC_replicate3
62 =========== ================
63
64 IThe output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'.
65 The names in column 2 must match the names given to the datasets in your history.
66 ]]></help>
67 <expand macro="citation"/>
68 </tool>