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comparison Recount.xml @ 6:3ce32282f6a4 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 228bd64b01f184d5d8ebc9f65fe0add2d45ed4fe
author sblanck
date Tue, 26 Jun 2018 08:54:45 -0400
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5:ca46ad51fe5a 6:3ce32282f6a4
1 <tool id="Recount" name="Recount" version="1.0.0">
2
3 <description>Get rna-seq count data with R recount Package</description>
4
5 <requirements>
6 <requirement type="package">bioconductor-recount</requirement>
7 <requirement type="package">r-optparse</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <regex match="Warning" source="both" level="warning"/>
12 </stdio>
13
14 <command>
15 <![CDATA[
16 Rscript --vanilla
17 ${__tool_directory__}/Recount.R
18 --id ${recountID}
19 --report ${report}
20 ]]>
21 </command>
22
23 <inputs>
24 <param name="recountID" type="text" size="12" optional="false" label="Recount ID" help="">
25 <validator type="empty_field"/>
26 </param>
27 </inputs>
28
29 <outputs>
30 <data format="txt" name="report">
31 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="split" visible="true" />
32 </data>
33 </outputs>
34
35 <tests>
36 </tests>
37
38 <help>
39 <![CDATA[
40 **What it does**
41
42 This tool fetches RNA-seq count data directly from Recount project based on the recount bioconductor R package. Given an ID, it returns a small report
43 containing the metadata of the experiment. Il also generates one count file per sample.
44
45 **Results**
46
47 - Tabular file containing samples ID and samples conditions
48 - One count file per sample
49 ]]>
50 </help>
51
52 </tool>