Mercurial > repos > xuebing > kplogo

comparison kplogo.xml @ 4:00b951fec5f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 24 Mar 2017 16:49:23 -0400
parents 7c3170671f1b
children 89aa9e0df5d4
comparison
equal deleted inserted replaced
3:7c3170671f1b 4:00b951fec5f7
1 <tool id="kplogo" name="kpLogo" version="1.0"> 1 <tool id="kplogo" name="kpLogo" version="1.0">
2 <description>for positional k-mer analysis</description> 2 <description>for positional k-mer analysis</description>
3 <command> 3 <command>
4 4
5 kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end 2> tmp; 5 kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end
6 #if $background.background_model == '-bg'
7 -bgfile $background_input
8 #else
9 $background.background_model
10 #end if
11 2> tmp;
6 cp ${output}.most.significant.each.position.pdf $output; 12 cp ${output}.most.significant.each.position.pdf $output;
7 cp ${output}.pdf $logo_prob; 13 cp ${output}.pdf $logo_prob;
8 cp ${output}.info.pdf $logo_info; 14 cp ${output}.info.pdf $logo_info;
9 cp ${output}.freq.pdf $logo_freq; 15 cp ${output}.freq.pdf $logo_freq;
10 cp ${output}.most.significant.each.position.txt $tab_most; 16 cp ${output}.most.significant.each.position.txt $tab_most;
53 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option> 59 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
54 <option value="">None (no degenerate residuals)</option> 60 <option value="">None (no degenerate residuals)</option>
55 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option> 61 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
56 </param> 62 </param>
57 63
64
65
66 <conditional name="background">
67 <param name="background_model" type="select" label="Background model (only for unweighted sequences)">
68 <option value="" selected="True">Average across all positions in input sequences</option>
69 <option value="-shuffle 100,2">Shuffle each input sequence 100 times preserving di-residual frequency</option>
70 <option value="-markov 1">Markov model learned from input sequences, first order</option>
71 <option value="-bg">Background sequences (not supported yet in Galaxy)</option>
72 </param>
73 <when value="-bg">
74 <param format="text" name="background_input" type="data" label="Background sequences (FASTA or Tabular)" />
75 </when>
76 </conditional>
77
78
79
58 <param name="startPos" type="integer" value="1" label="Redefine position 1. The positions before it will be numbered as -1, -2, etc (no 0)." /> 80 <param name="startPos" type="integer" value="1" label="Redefine position 1. The positions before it will be numbered as -1, -2, etc (no 0)." />
59 81
60 <param name="fix" type="float" value="0.75" label="Fixation frequency"/> 82 <param name="fix" type="float" value="0.75" label="Fixation frequency"/>
61 83
62 </page> 84 </page>