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comparison lasttrain.xml @ 3:3de2195f32c0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
author iuc
date Fri, 13 Nov 2020 09:05:49 +0000
parents 86206f93fb13
children 8705e0d74a0f
comparison
equal deleted inserted replaced
2:bf30030e5265 3:3de2195f32c0
1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> 1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01">
2 2
3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description> 3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros_last.xml</import> 6 <import>macros_last.xml</import>
16 #end if 16 #end if
17 17
18 last-train 18 last-train
19 19
20 -Q $init_options.Q 20 -Q $init_options.Q
21
22 -r $init_options.r 21 -r $init_options.r
23 -q $init_options.q 22 -q $init_options.q
24
25 -a $init_options.cost_opt.a 23 -a $init_options.cost_opt.a
26 -b $init_options.cost_opt.b 24 -b $init_options.cost_opt.b
27 -A $init_options.cost_opt.A 25 -A $init_options.cost_opt.A
28 -B $init_options.cost_opt.B 26 -B $init_options.cost_opt.B
29
30 -D $last_train_opt.align_opt.D 27 -D $last_train_opt.align_opt.D
31 -E $last_train_opt.align_opt.E 28 #if $last_train_opt.align_opt.E != ""
29 -E $last_train_opt.align_opt.E
30 #end if
32 -s $last_train_opt.align_opt.s 31 -s $last_train_opt.align_opt.s
33 -S $last_train_opt.align_opt.S 32 -S $last_train_opt.align_opt.S
34 -T $last_train_opt.align_opt.T 33 -T $last_train_opt.align_opt.T
35 -m $last_train_opt.align_opt.m 34 -m $last_train_opt.align_opt.m
36 -k $last_train_opt.align_opt.k 35 -k $last_train_opt.align_opt.k
72 71
73 <section name="last_train_opt" title="Last-train options" expanded="false"> 72 <section name="last_train_opt" title="Last-train options" expanded="false">
74 <!-- Training options missing --> 73 <!-- Training options missing -->
75 <section name="align_opt" title="Alignment options" expanded="true"> 74 <section name="align_opt" title="Alignment options" expanded="true">
76 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/> 75 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
77 <param argument="-E" type="integer" value="10" label="Maximum expected alignments per square giga"/> 76 <param argument="-E" type="integer" value="" optional="true" label="Maximum expected alignments per square giga"/>
78 <param argument="-s" type="select" multiple="false" label="Query strand to use"> 77 <param argument="-s" type="select" multiple="false" label="Query strand to use">
79 <option value="0">Reverse</option> 78 <option value="0">Reverse</option>
80 <option value="1" selected="true">Forward</option> 79 <option value="1" selected="true">Forward</option>
81 <option value="2">Both</option> 80 <option value="2">Both</option>
82 </param> 81 </param>
109 <test> 108 <test>
110 <conditional name="db_opts"> 109 <conditional name="db_opts">
111 <param name="db_opts_input" value="db"/> 110 <param name="db_opts_input" value="db"/>
112 <param name="database" value="humdb"/> 111 <param name="database" value="humdb"/>
113 </conditional> 112 </conditional>
113 <section name="last_train_opt">
114 <section name="align_opt">
115 <param name="E" value="10"/>
116 </section>
117 </section>
118 <param name="query_fasta" value="fuguMito.fa"/>
119 <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/>
120 </test>
121 <test>
122 <conditional name="db_opts">
123 <param name="db_opts_input" value="db"/>
124 <param name="database" value="humdb"/>
125 </conditional>
114 <param name="query_fasta" value="fuguMito.fa"/> 126 <param name="query_fasta" value="fuguMito.fa"/>
115 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/> 127 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
116 </test> 128 </test>
117 </tests> 129 </tests>
118 130