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comparison rp2biosensor.xml @ 1:3ff2af8163f0 draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Fri, 25 Feb 2022 07:14:49 +0000
parents 4714b9d825d1
children f7dc0fcaf839
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0:4714b9d825d1 1:3ff2af8163f0
1 <tool id="rp2biosensor" name="rp2biosensor" version="1.0.1"> 1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09">
2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description> 2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.1.0</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.0.1">rp2biosensor</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 python -m rp2biosensor 10 python -m rp2biosensor
8 '$rp2_results' 11 '$rp2_results'
9 --opath '$html_file' 12 --opath '$html_file'
13 #if str($adv.json_graph) == "true"
14 --ojson '$json_file'
15 #end if
10 ]]></command> 16 ]]></command>
11 <inputs> 17 <inputs>
12 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/> 18 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
19 <section name="adv" title="Advanced Options" expanded="false">
20 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
21 </section>
13 </inputs> 22 </inputs>
14 <outputs> 23 <outputs>
15 <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/> 24 <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
25 <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
26 <filter> adv['json_graph'] </filter>
27 </data>
16 </outputs> 28 </outputs>
17 <tests> 29 <tests>
18 <test> 30 <test>
19 <!-- test 1: check if identical outputs are produced --> 31 <!-- test 1: check if identical outputs are produced -->
20 <param name="rp2_results" value="rp2-results_dmax-16.csv" /> 32 <param name="rp2_results" value="rp2-results-lactate.csv" />
21 <output name="html_file" md5="4abb29e769106e75e68a939764dd2e31"/> 33 <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/>
22 </test> 34 </test>
23 </tests> 35 </tests>
24 <help><![CDATA[ 36 <help><![CDATA[
25 rp2biosensor 37 rp2biosensor
26 ================ 38 ================
37 Output 49 Output
38 ------ 50 ------
39 51
40 * **opath**\ : (string) Output path. Default: biosensor.html. 52 * **opath**\ : (string) Output path. Default: biosensor.html.
41 53
42 * **o_sbol_dir**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file. 54 * **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.
55
56 * **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None
43 57
44 Project Links 58 Project Links
45 ------------------ 59 ------------------
46 60
47 * `GitHub <https://github.com/brsynth/rp2biosensor>`_ 61 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
48 62
49 Version 63 Version
50 ---------- 64 ----------
51 65
52 1.0.1 66 2.1.0
53 67
54 Authors 68 Authors
55 ------- 69 -------
56 70
57 * **Thomas Duigou** 71 * **Thomas Duigou**