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comparison rp2biosensor.xml @ 2:f7dc0fcaf839 draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Mon, 07 Mar 2022 13:44:07 +0000
parents 3ff2af8163f0
children bd4fe7af0157
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1:3ff2af8163f0 2:f7dc0fcaf839
1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09"> 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> 3 <macros>
4 <token name="@TOOL_VERSION@">2.1.0</token> 4 <token name="@TOOL_VERSION@">3.0.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 python -m rp2biosensor 10 python -m rp2biosensor
11 '$rp2_results' 11 '$rp2_results'
12 '$sink_file'
12 --opath '$html_file' 13 --opath '$html_file'
13 #if str($adv.json_graph) == "true" 14 #if str($adv.json_graph) == "true"
14 --ojson '$json_file' 15 --ojson '$json_file'
15 #end if 16 #end if
16 ]]></command> 17 ]]></command>
17 <inputs> 18 <inputs>
18 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/> 19 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
20 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
19 <section name="adv" title="Advanced Options" expanded="false"> 21 <section name="adv" title="Advanced Options" expanded="false">
20 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" /> 22 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
21 </section> 23 </section>
22 </inputs> 24 </inputs>
23 <outputs> 25 <outputs>
43 ----- 45 -----
44 46
45 Required: 47 Required:
46 48
47 * **rp2_results**\ : (string) RetroPath2.0 results. 49 * **rp2_results**\ : (string) RetroPath2.0 results.
50 * **sink_file**\ : (string) Sink file used for RetroPath2.0.
48 51
49 Output 52 Output
50 ------ 53 ------
51 54
52 * **opath**\ : (string) Output path. Default: biosensor.html. 55 * **opath**\ : (string) Output path. Default: biosensor.html.
61 * `GitHub <https://github.com/brsynth/rp2biosensor>`_ 64 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
62 65
63 Version 66 Version
64 ---------- 67 ----------
65 68
66 2.1.0 69 3.0.0
67 70
68 Authors 71 Authors
69 ------- 72 -------
70 73
71 * **Thomas Duigou** 74 * **Thomas Duigou**