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comparison tophat2_wrapper.xml @ 9:0849fa93eadb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
author devteam
date Sun, 01 Jan 2017 06:51:32 -0500
parents 758594ed0364
children 16c4255042be
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8:758594ed0364 9:0849fa93eadb
93 --no-novel-indels 93 --no-novel-indels
94 #end if 94 #end if
95 95
96 ## Supplying junctions parameters. 96 ## Supplying junctions parameters.
97 #if $params.own_junctions.use_junctions == "Yes": 97 #if $params.own_junctions.use_junctions == "Yes":
98 #if $params.own_junctions.gene_model_ann.use_annotations == "Yes": 98 #if $params.own_junctions.gene_model_ann.use_annotations == "indexed"
99 -G $params.own_junctions.gene_model_ann.gene_annotation_model.fields.path
100 #elif $params.own_junctions.gene_model_ann.use_annotations == "history"
99 -G $params.own_junctions.gene_model_ann.gene_annotation_model 101 -G $params.own_junctions.gene_model_ann.gene_annotation_model
100 #end if 102 #end if
101 #if $params.own_junctions.raw_juncs.use_juncs == "Yes": 103 #if $params.own_junctions.raw_juncs.use_juncs == "Yes":
102 -j $params.own_junctions.raw_juncs.raw_juncs 104 -j $params.own_junctions.raw_juncs.raw_juncs
103 #end if 105 #end if