Mercurial > repos > iuc > idr

annotate idr.xml @ 1:56db0f88477e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
author iuc
date Mon, 23 Nov 2020 22:50:50 +0000
parents 31392f890eaf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
2 <tool id="idr" name="IDR" version="@VERSION@">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
3 <description>compare ranked list of identifications</description>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
4 <macros>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
5 <token name="@VERSION@">2.0.3</token>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
6 </macros>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
7 <requirements>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
8 <requirement type="package" version="@VERSION@">idr</requirement>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
9 </requirements>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
10 <command detect_errors="aggressive">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
11 <![CDATA[
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
12 idr --samples '$primus' '$secundus'
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
13 #if $peak_list:
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
14 --peak-list '$peak_list'
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
15 #end if
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
16 #if $input_file_type:
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
17 #if $primus.dataset.ext == 'gff':
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
18 --input-file-type gff
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
19 #else:
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
20 --input-file-type $input_file_type
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
21 #end if
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
22 #end if
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
23 #if $idr_threshold:
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
24 --idr-threshold $idr_threshold
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
25 #end if
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
26 #if $rank != 'default':
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
27 --rank $rank
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
28 #end if
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
29 --output-file idrValues.bed
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
30 --soft-idr-threshold $soft_idr_threshold
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
31 $plot $use_nonoverlapping_peaks --peak-merge-method $peak_merge_method
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
32 --initial-mu $initial_mu --initial-sigma $initial_sigma --initial-rho $initial_rho
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
33 --initial-mix-param $initial_mix_param $fix_mu $fix_sigma
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
34 $dont_filter_peaks_below_noise_mean $use_best_multisummit_idr
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
35 $allow_negative_scores --random-seed $random_seed --max-iter $max_iter
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
36 --convergence-eps $convergence_eps $only_merge_peaks
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
37 ]]>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
38 </command>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
39 <inputs>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
40 <param name="primus" argument="--samples" type="data" format="bed,gff" label="First set of peaks in GFF or BED format" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
41 <param name="secundus" argument="--samples" type="data" format="bed,gff" label="Second set of peaks in GFF or BED format" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
42 <param name="peak_list" argument="--peak-list" type="data" format="bed,gff" optional="True" label="List of peaks to filter by" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
43 <param name="input_file_type" argument="--input-file-type" type="select" label="Input BED format" help="This option is ignored if the input file is GFF">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
44 <option value="" selected="true">Vanilla BED</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
45 <option value="gff">GFF</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
46 <option value="broadPeak">ENCODE broadPeak</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
47 <option value="narrowPeak">ENCODE narrowPeak</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
48 </param>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
49 <param argument="--rank" type="select" label="Column to use for ranking peaks">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
50 <option value="default">Use default</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
51 <option value="signal.value">signal</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
52 <option value="p.value">p value</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
53 <option value="q.value">q value</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
54 </param>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
55 <param name="idr_threshold" argument="--idr-threshold" type="float" optional="true" value="" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
56 <param name="soft_idr_threshold" argument="--soft-idr-threshold" type="float" value="0.05" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
57 <param argument="--plot" type="boolean" truevalue="--plot" falsevalue="" label="Output PNG plot of peaks" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
58 <param name="use_nonoverlapping_peaks" argument="--use-nonoverlapping-peaks" type="boolean" truevalue="--use-nonoverlapping-peaks" falsevalue="" label="Use peaks without an overlapping match and set the value to 0" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
59 <param name="peak_merge_method" argument="--peak-merge-method" type="select" label="Method to use for merging peaks">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
60 <option value="sum">Sum</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
61 <option value="avg">Average</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
62 <option value="min">Min</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
63 <option value="max">Max</option>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
64 </param>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
65 <param name="initial_mu" argument="--initial-mu" type="float" value="0.1" label="Initial value of mu" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
66 <param name="initial_sigma" argument="--initial-sigma" type="float" value="1.0" label="Initial value of sigma" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
67 <param name="initial_rho" argument="--initial-rho" type="float" value="0.2" label="Initial value of rho" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
68 <param name="initial_mix_param" argument="--initial-mix-param" type="float" value="0.5" label="Initial value of the mixture parameters" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
69 <param name="fix_mu" argument="--fix-mu" type="boolean" truevalue="--fix-mu" falsevalue="" label="Fix mu to the starting point and do not let it vary" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
70 <param name="fix_sigma" argument="--fix-sigma" type="boolean" truevalue="--fix-sigma" falsevalue="" label="Fix sigma to the starting point and do not let it vary" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
71 <param name="dont_filter_peaks_below_noise_mean" argument="--dont-filter-peaks-below-noise-mean" type="boolean" truevalue="--dont-filter-peaks-below-noise-mean" falsevalue="" label="Allow signal points that are below the noise mean" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
72 <param name="use_best_multisummit_idr" argument="--use-best-multisummit-IDR" type="boolean" truevalue="--use-best-multisummit-IDR" falsevalue="" label="Set the IDR value for a group of multi summit peaks" help="A group of peaks with the same chr/start/stop but different summits" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
73 <param name="allow_negative_scores" argument="--allow-negative-scores" type="boolean" truevalue="--allow-negative-scores" falsevalue="" label="Allow negative values for scores" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
74 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="The random seed value" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
75 <param name="max_iter" argument="--max-iter" type="integer" value="3000" label="The maximum number of optimization iterations" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
76 <param name="convergence_eps" argument="--convergence-eps" type="float" value="0.000001" label="The maximum change in parameter value changes for convergence" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
77 <param name="only_merge_peaks" argument="--only-merge-peaks" type="boolean" truevalue="--only-merge-peaks" falsevalue="" label="Only return the merged peak list" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
78 </inputs>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
79 <outputs>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
80 <data format="bed" name="idr_values" from_work_dir="idrValues.bed" label="${tool.name} on ${on_string}: IDR Values">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
81 <actions>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
82 <action type="format">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
83 <option type="from_param" name="primus" param_attribute="ext" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
84 </action>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
85 </actions>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
86 </data>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
87 <data format="png" name="idr_plot" from_work_dir="idrValues.bed.png" label="${tool.name} on ${on_string}: PNG Plot">
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
88 <filter>plot</filter>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
89 </data>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
90 </outputs>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
91 <tests>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
92 <test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
93 <param name="primus" value="idr_input1.1.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
94 <param name="secundus" value="idr_input1.2.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
95 <param name="rank" value="default" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
96 <param name="plot" value="True" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
97 <output name="idr_values" file="idr_out1.bed" ftype="bed" />
1
56db0f88477e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
iuc
parents: 0
diff changeset
98 <output name="idr_plot" file="idr_out1.png" ftype="png" compare="sim_size" delta="1000"/>
0
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
99 </test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
100 <test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
101 <param name="primus" value="idr_input2.1.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
102 <param name="secundus" value="idr_input2.2.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
103 <param name="rank" value="default" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
104 <param name="plot" value="True" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
105 <output name="idr_values" file="idr_out2.bed" ftype="bed" />
1
56db0f88477e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
iuc
parents: 0
diff changeset
106 <output name="idr_plot" file="idr_out2.png" ftype="png" compare="sim_size" delta="1000"/>
0
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
107 </test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
108 <test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
109 <param name="primus" value="idr_input3.1.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
110 <param name="secundus" value="idr_input3.2.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
111 <param name="peak_list" value="idr_input3.3.bed" ftype="bed" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
112 <param name="rank" value="default" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
113 <param name="plot" value="True" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
114 <output name="idr_values" file="idr_out3.bed" ftype="bed" />
1
56db0f88477e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
iuc
parents: 0
diff changeset
115 <output name="idr_plot" file="idr_out3.png" ftype="png" compare="sim_size" delta="1000"/>
0
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
116 </test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
117 <test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
118 <param name="primus" value="idr_input4.1.gff" ftype="gff" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
119 <param name="secundus" value="idr_input4.2.gff" ftype="gff" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
120 <param name="input_file_type" value="gff" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
121 <param name="rank" value="default" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
122 <param name="plot" value="True" />
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
123 <output name="idr_values" file="idr_out4.gff" ftype="gff" />
1
56db0f88477e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
iuc
parents: 0
diff changeset
124 <output name="idr_plot" file="idr_out4.png" ftype="png" compare="sim_size" delta="1000"/>
0
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
125 </test>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
126 </tests>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
127 <help>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
128 <![CDATA[
1
56db0f88477e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
iuc
parents: 0
diff changeset
129 The `IDR <https://github.com/nboley/idr/blob/master/README.md>`__ (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates.
0
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
130 ]]>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
131 </help>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
132 <citations>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
133 <citation type="doi">10.1214/11-AOAS466</citation>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
134 </citations>
31392f890eaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
parents:
diff changeset
135 </tool>