Mercurial > repos > rnateam > locarna_multiple

comparison locarna_multiple.xml @ 2:f8c5261fafdc draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:22:23 -0500
parents 3a4167720464
children
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1:3a4167720464 2:f8c5261fafdc
50 --plfold-winsize $Folding.plfold_winsize 50 --plfold-winsize $Folding.plfold_winsize
51 #end if 51 #end if
52 $Folding.alifold_consensus_dp 52 $Folding.alifold_consensus_dp
53 53
54 @HEURISTIC_ARGS@ 54 @HEURISTIC_ARGS@
55
56 #if str($alignment_mode.alignment_mode_selector) == "sparse"
57 --pw-aligner-options " @HEURISTIC_SPARSE_ARGS@ "
58 #end if
59
55 60
56 @CONSTRAINT_ARGS@ 61 @CONSTRAINT_ARGS@
57 #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes" 62 #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes"
58 --anchor-constraints $Constraints.bed_anchors.bed_anchors_file 63 --anchor-constraints $Constraints.bed_anchors.bed_anchors_file
59 #end if 64 #end if
90 > 95 >
91 <option value="global_locarna">Global alignment 96 <option value="global_locarna">Global alignment
92 (LocARNA)</option> 97 (LocARNA)</option>
93 <option value="local_locarna">Local alignment (LocARNA)</option> 98 <option value="local_locarna">Local alignment (LocARNA)</option>
94 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option> 99 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
95 <option value="sparse">Global alignment (SPARSE)</option> 100 <option value="sparse">Global fast alignment (SPARSE)</option>
96 </param> 101 </param>
97 <when value="global_locarna"> 102 <when value="global_locarna">
98 <param name="free_endgaps" type="select" label="Free endgaps" 103 <param name="free_endgaps" type="select" label="Free endgaps"
99 help="Specify whether gaps at the ends (all, 5', or 3' ends) 104 help="Specify whether gaps at the ends (all, 5', or 3' ends)
100 of the sequences should be penalized or allowed for free."> 105 of the sequences should be penalized or allowed for free.">
117 help="--iterate" /> 122 help="--iterate" />
118 <param name="iterations" type="integer" 123 <param name="iterations" type="integer"
119 value="1" label="Number of refinement iterations" 124 value="1" label="Number of refinement iterations"
120 help="--iterations num" /> 125 help="--iterations num" />
121 </when> 126 </when>
122 <when value="sparse" /> 127 <when value="sparse">
128 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
129 <expand macro="common_heuristic_parameters_sparse" />
130 </section>
131 </when>
132
123 </conditional> 133 </conditional>
124 134
125 <param name="outputs" type="select" display="checkboxes" multiple="True" 135 <param name="outputs" type="select" display="checkboxes" multiple="True"
126 label="Output options"> 136 label="Output options">
127 <option value="clustal_strict" selected="True">Output alignment 137 <option value="clustal_strict" selected="True">Output alignment