Mercurial > repos > proteore > proteore_maps_visualization

comparison kegg_maps_visualization.xml @ 3:f4938e47f2f8 draft

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planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
author proteore
date Tue, 18 Dec 2018 09:38:13 -0500
parents 8a6863adcd09
children 4cc2265d1294
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2:8a6863adcd09 3:f4938e47f2f8
1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18"> 1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18.1">
2 <description>of (differentially expressed) genes/proteins</description> 2 <description>of (differentially expressed) genes/proteins</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> 4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> 5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
6 </requirements> 6 </requirements>
11 #else 11 #else
12 --input="$input.file" 12 --input="$input.file"
13 --id_column="$input.ncol" 13 --id_column="$input.ncol"
14 --header="$input.header" 14 --header="$input.header"
15 #end if 15 #end if
16 #if $pathways_section.species.pathways.pathways_id != "pathways_file" 16 #if $species.pathways.pathways_id != "pathways_file"
17 --pathways_id="$pathways_section.species.pathways.pids" 17 --pathways_id="$species.pathways.pids"
18 #else 18 #else
19 --pathways_input="$pathways_section.species.pathways.file" 19 --pathways_input="$species.pathways.file"
20 --header2="$pathways_section.species.pathways.header2" 20 --header2="$species.pathways.header2"
21 --pathway_col="$pathways_section.species.pathways.ncol2" 21 --pathway_col="$species.pathways.ncol2"
22 #end if 22 #end if
23 --id_type="$id_type" 23 --id_type="$id_type"
24 --native_kegg="$native" 24 --native_kegg="$native"
25 25
26 26
29 --fold_change_col="$input.foldchange.fc_col" 29 --fold_change_col="$input.foldchange.fc_col"
30 #else 30 #else
31 --fold_change_data="false" 31 --fold_change_data="false"
32 #end if 32 #end if
33 33
34 --species=${pathways_section.species.ref_file} 34 --species=${species.ref_file}
35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $pathways_section.species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } 35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
36 --output="$text_output" 36 --output="$text_output"
37 37
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <!--section name="pathways_section" title="Pathways" expanded="True"--> 40 <!--section name="pathways_section" title="Pathways" expanded="True"-->