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comparison lcrgenie.xml @ 1:afbbecdcc0e3 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 03 Feb 2022 13:30:30 +0000
parents 71568c0c83f4
children 6f447c1584bf
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0:71568c0c83f4 1:afbbecdcc0e3
1 <tool id="LCRGenie" name="LCR Genie" version="1.0.1"> 1 <tool id="LCRGenie" name="LCR Genie" version="@TOOL_VERSION@" profile="19.09">
2 <description>Ligase Chain Reaction</description> 2 <description>Ligase Chain Reaction</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.2</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.0.1">lcr_genie</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">lcr_genie</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <regex match="WARNING:" level="warning" /> 10 <regex match="WARNING:" level="warning" />
8 <regex match="ERROR:" level="fatal" /> 11 <regex match="ERROR:" level="fatal" />
9 </stdio> 12 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
11 python -m lcr_genie 14 python -m lcr_genie
12 '$LCR_input' 15 '$LCR_input'
13 '$LCR_output' 16 out.xlsx
14 --melting_temp '$adv.melting_temp' 17 --melting_temp '$adv.melting_temp'
18 && cp out.xlsx '$LCR_output'
15 ]]></command> 19 ]]></command>
16 <inputs> 20 <inputs>
17 <param name="LCR_input" type="data" format="xml" label="Constructs" /> 21 <param name="LCR_input" type="data" format="xml" label="Constructs" />
18 <section name="adv" title="Advanced Options" expanded="false"> 22 <section name="adv" title="Advanced Options" expanded="false">
19 <param name="melting_temp" value="60.0" type="float" label="Target melting temperature for the bridging oligos" /> 23 <param name="melting_temp" value="60.0" type="float" label="Target melting temperature for the bridging oligos" />
24 </outputs> 28 </outputs>
25 <tests> 29 <tests>
26 <test> 30 <test>
27 <!-- test 1: check if identical outputs are produced with default parameters --> 31 <!-- test 1: check if identical outputs are produced with default parameters -->
28 <param name="LCR_input" value="LCR_input_lycopene.xml" /> 32 <param name="LCR_input" value="LCR_input_lycopene.xml" />
29 <output name="LCR_output" file="LCR_output_lycopene.xlsx" ftype="xlsx" compare="sim_size" /> 33 <output name="LCR_output" >
34 <assert_contents>
35 <has_size value="58196" delta="100" />
36 </assert_contents>
37 </output>
30 </test> 38 </test>
31 </tests> 39 </tests>
32 <help><![CDATA[ 40 <help><![CDATA[
33 LCRGenie 41 LCRGenie
34 ======== 42 ========
53 * `GitHub <https://github.com/neilswainston/LCRGenie/>`_ 61 * `GitHub <https://github.com/neilswainston/LCRGenie/>`_
54 62
55 Version 63 Version
56 ---------- 64 ----------
57 65
58 1.0.1 66 1.0.2
59 67
60 Authors 68 Authors
61 ------- 69 -------
62 70
63 * **Neil Swainston** 71 * **Neil Swainston**