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comparison goprofiles.xml @ 5:781072a65600 draft

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planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
author proteore
date Wed, 19 Sep 2018 05:49:06 -0400
parents 715002a394ec
children 6afe8166a9a4
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4:715002a394ec 5:781072a65600
1 <tool id="goProfiles" name="goProfiles" version="0.1.0"> 1 <tool id="goProfiles" name="goProfiles" version="2018.09.04">
2 <description> Statistical analysis of functional profiles 2 <description>Statistical analysis of functional profiles</description>
3 </description> 3 <requirements>
4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement> 4 <requirement type="package" version="3.4.1">R</requirement>
6 <requirement type="package" version="3.4.1">bioconductor-org.hs.eg.db</requirement> 5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
7 <requirement type="package" version="1.38.2">bioconductor-annotationdbi</requirement> 6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
8 <requirement type="package" version="2.36.2">bioconductor-biobase</requirement> 7 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
8 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
9 <requirement type="package" version="1.38.0">goprofiles</requirement> 9 <requirement type="package" version="1.38.0">goprofiles</requirement>
10 </requirements> 10 </requirements>
11 <stdio> 11 <stdio>
12 <exit_code range="1:" /> 12 <exit_code range="1:" />
13 </stdio> 13 </stdio>
36 --title="$title" 36 --title="$title"
37 37
38 --duplicate="$duplicate" 38 --duplicate="$duplicate"
39 39
40 --text_output="$text_output" 40 --text_output="$text_output"
41
42 --species="$species"
41 43
42 ]]></command> 44 ]]></command>
43 <inputs> 45 <inputs>
44 <conditional name="input" > 46 <conditional name="input" >
45 <param name="ids" type="select" label="Enter your ID list (only Entrez Gene ID or UniProt accession number allowed" help="Copy/paste or ID list from a file (e.g. table)" > 47 <param name="ids" type="select" label="Enter your ID list (only Entrez Gene ID or UniProt accession number allowed" help="Copy/paste or ID list from a file (e.g. table)" >
71 <option value="UniProt">UniProt protein ID</option> 73 <option value="UniProt">UniProt protein ID</option>
72 </param> 74 </param>
73 </when> 75 </when>
74 </conditional> 76 </conditional>
75 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" /> 77 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
78 <param name="species" type="select" label="Select your species">
79 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
80 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
81 </param>
76 <param type="select" name="onto_opt" label="Please select GO terms category" multiple="True" display="checkboxes" > 82 <param type="select" name="onto_opt" label="Please select GO terms category" multiple="True" display="checkboxes" >
77 <option value="CC">Cellular Component (CC)</option> 83 <option value="CC">Cellular Component (CC)</option>
78 <option value="MF">Molecular Function (MF)</option> 84 <option value="MF">Molecular Function (MF)</option>
79 <option value="BP">Biological Process (BP)</option> 85 <option value="BP">Biological Process (BP)</option>
80 </param> 86 </param>
92 <option value="PDF" selected="True">PDF</option> 98 <option value="PDF" selected="True">PDF</option>
93 </param> 99 </param>
94 </section> 100 </section>
95 </inputs> 101 </inputs>
96 <outputs> 102 <outputs>
97 <collection type="list" label="GO Profile diagram outputs" name="output" > 103 <collection type="list" label="GO Profile diagram output" name="output" >
98 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" /> 104 <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
99 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" /> 105 <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
100 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" /> 106 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
101 </collection> 107 </collection>
102 <data name="text_output" format="tabular" label="GO Profile text output" /> 108 <data name="text_output" format="tabular" label="GO Profile text output" />
103 </outputs> 109 </outputs>
104 <tests> 110 <tests>
105 <test> 111 <test>
106 <conditional name="input"> 112 <conditional name="input">
107 <param name="ids" value="file" /> 113 <param name="ids" value="file" />
108 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" /> 114 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
109 <param name="ncol" value="c1" /> 115 <param name="ncol" value="c1" />
110 <param name="header" value="talse" /> 116 <param name="header" value="true" />
111 <param name="id_type" value="UniProt" /> 117 <param name="id_type" value="UniProt" />
112 </conditional> 118 </conditional>
113 <param name="duplicate" value="false"/> 119 <param name="duplicate" value="false"/>
114 <param name="onto_opt" value="CC,MF,BP" /> 120 <param name="onto_opt" value="CC,MF,BP" />
115 <param name="level" value="2" /> 121 <param name="level" value="2" />
117 <param name="title" value="Test" /> 123 <param name="title" value="Test" />
118 <section name="opt" > 124 <section name="opt" >
119 <param name="plot_opt" value="PDF" /> 125 <param name="plot_opt" value="PDF" />
120 </section> 126 </section>
121 <output_collection name="output" type="list" > 127 <output_collection name="output" type="list" >
122 <element name="GO_Profile_diagram_outputs__profile.BP.pdf" file="GO_Profile_diagram_outputs__profile.BP.pdf" ftype="pdf" /> 128 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
123 <element name="GO_Profile_diagram_outputs__profile.CC.pdf" file="GO_Profile_diagram_outputs__profile.CC.pdf" ftype="pdf" /> 129 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
124 <element name="GO_Profile_diagram_outputs__profile.MF.pdf" file="GO_Profile_diagram_outputs__profile.MF.pdf" ftype="pdf" /> 130 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
125 </output_collection> 131 </output_collection>
126 <output name="text_output" file="GO_Profile_text_output.txt"/> 132 <output name="text_output" file="GO_Profile_text_output.txt"/>
127 </test> 133 </test>
128 </tests> 134 </tests>
129 <help><![CDATA[ 135 <help><![CDATA[