Mercurial > repos > rnateam > peakachu
annotate peakachu.xml @ 0:bc594df2aba3 draft
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
author | rnateam |
---|---|
date | Thu, 15 Feb 2018 15:59:41 -0500 |
parents | |
children | 68656d100a7f |
rev | line source |
---|---|
0
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
1 <tool id="peakachu" name="PEAKachu" version="0.1.0.0"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
2 <description>Calls Peaks in CLIP data</description> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
3 <requirements> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
4 <requirement type="package" version="3.6">python</requirement> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
5 <requirement type="package" version="0.1.0">peakachu</requirement> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
6 </requirements> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
7 <version_command> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
8 <![CDATA[ |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
9 peakachu --version |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
10 ]]> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
11 </version_command> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
12 <command detect_errors="aggressive"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
13 <![CDATA[ |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
14 #for $i, $clib in enumerate($controlLibs): |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
15 #if $clib: |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
16 ln -s -f '$clib' ${i}.c.bam && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
17 ln -s -f '$clib.metadata.bam_index' ${i}.c.bam.bai && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
18 #end if |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
19 #end for |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
20 #for $j, $elib in enumerate($experimentLibs): |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
21 ln -s -f '$elib' ${j}.e.bam && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
22 ln -s -f '$elib.metadata.bam_index' ${j}.e.bam.bai && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
23 #end for |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
24 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
25 pwd && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
26 mkdir ./tmp_output && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
27 peakachu |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
28 ${mode.mode_selector} |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
29 --exp_libs |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
30 #for $i, $elib in enumerate($experimentLibs): |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
31 '${i}.e.bam' |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
32 #end for |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
33 #for $i, $clib in enumerate($controlLibs): |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
34 #if $clib and $i == 0: |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
35 --ctr_libs |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
36 #end if |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
37 #if $clib: |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
38 '${i}.c.bam' |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
39 #end if |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
40 #end for |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
41 $pairwise_replicates |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
42 $paired_end |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
43 --max_insert_size $max_insert_size |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
44 --features '$features' |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
45 --sub_features '$sub_features' |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
46 --max_proc "\${GALAXY_SLOTS:-1}" |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
47 --output_folder ./tmp_output |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
48 #if str($mode.mode_selector) == 'adaptive': |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
49 --min_cluster_expr_frac $mode.min_cluster_expr_frac |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
50 --min_block_overlap $mode.min_block_overlap |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
51 --min_max_block_expr $mode.min_max_block_expr |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
52 #elif str($mode.mode_selector) == 'window': |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
53 --window_size $mode.window_size |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
54 --step_size $mode.step_size |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
55 --stat_test $mode.stat_test |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
56 --het_p_val_threshold $mode.het_p_val_threshold |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
57 --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
58 #end if |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
59 --norm_method $mode.norm_method.norm_method_selector |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
60 #if str($mode.norm_method.norm_method_selector) == 'manual': |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
61 --size_factors $size_factors |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
62 #end if |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
63 --mad_multiplier $mad_multiplier |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
64 --fc_cutoff $fc_cutoff |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
65 --padj_threshold $padj_threshold |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
66 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
67 && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
68 head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
69 tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
70 mv peaks.tsv '$peak_tables' && |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
71 mv ./tmp_output/plots/Initial*.png '$MA_plot' |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
72 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
73 ]]> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
74 </command> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
75 <inputs> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
76 <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
77 <param name="controlLibs" type="data" format="bam" label="Control Libraries" multiple="True" optional="True"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
78 <param argument="--pairwise_replicates" type="boolean" truevalue="--pairwise_replicates" falsevalue="" checked="False" label="Pairwise Replicates" /> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
79 <param argument="--paired_end" type="boolean" truevalue="--paired_end" falsevalue="" checked="False" label="Paired End" /> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
80 <param argument="--max_insert_size" type="integer" value="50" label="Maximum Insert Size"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
81 <!-- The gff feature is not implemented, because the function can easily be accomplished with featureCount or other tools |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
82 <param name="gffs" type="data" format="gff" label="Annotation" optional="True" multiple="True"/--> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
83 <param argument="--features" type="text" label="Features"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
84 <sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
85 <valid initial="default"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
86 </sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
87 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
88 <param argument="--sub_features" type="text" label="Sub-Features"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
89 <sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
90 <valid initial="default"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
91 </sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
92 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
93 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
94 <conditional name="mode"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
95 <param name="mode_selector" type="select" label="Select Mode" help="These modes work differently."> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
96 <option value="adaptive" selected="True">Adaptive</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
97 <option value="window">Window</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
98 <!-- The following options are not implemented because they are vastly different and should be implemented as their own tool, if need be. |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
99 <option value="coverage">Coverage</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
100 <option value="consensus_peak">Consensus Peak</option--> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
101 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
102 <when value="adaptive"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
103 <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
104 <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
105 <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
106 <conditional name="norm_method"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
107 <param name="norm_method_selector" type="select" label="Normalisation Method."> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
108 <option value="deseq" selected="True">DESeq2</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
109 <option value="manual">Manual</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
110 <option value="none">None</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
111 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
112 <when value="deseq"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
113 <when value="none"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
114 <when value="manual"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
115 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
116 <sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
117 <valid initial="default"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
118 </sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
119 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
120 </when> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
121 </conditional> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
122 </when> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
123 <when value="window"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
124 <param argument="--window_size" label="Window Size" type="integer" value="25"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
125 <param argument="--step_size" label="Step Size" type="integer" value="5"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
126 <param name="stat_test" type="select" label="Statistical Test"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
127 <option value="gtest" selected="True">gtest</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
128 <option value="deseq">DESeq2</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
129 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
130 <conditional name="norm_method"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
131 <param name="norm_method_selector" type="select" label="Normalisation Method."> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
132 <option value="tmm" selected="True">TMM</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
133 <option value="deseq">DESeq2</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
134 <option value="count">Count</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
135 <option value="manual">Manual</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
136 <option value="none">None</option> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
137 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
138 <when value="deseq"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
139 <when value="tmm"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
140 <when value="count"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
141 <when value="none"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
142 <when value="manual"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
143 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE"> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
144 <sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
145 <valid initial="default"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
146 </sanitizer> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
147 </param> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
148 </when> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
149 </conditional> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
150 <param argument="--het_p_val_threshold" label="Heterogeneous p-value Threshold" type="float" value="0.01"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
151 <param argument="--rep_pair_p_val_threshold" label="Paired p-value Threshold" type="float" value="0.05"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
152 </when> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
153 </conditional> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
154 <param argument="--mad_multiplier" label="Mad Multiplier" type="float" value="2.0"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
155 <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
156 <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
157 </inputs> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
158 <outputs> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
159 <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
160 <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
161 </outputs> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
162 <tests> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
163 <test> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
164 <param name="experimentLibs" value="test1_+xl.bam"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
165 <param name="controlLibs" value="test1_-xl.bam"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
166 <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
167 <output name="MA_plot" ftype="png" file="test1_MA.png"/> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
168 </test> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
169 </tests> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
170 <help> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
171 <![CDATA[ |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
172 **PEAKachu** |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
173 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
174 PEAKachu is a tool for the accurate mapping of RBP binding sites based on CLIP-seq and RIP-seq data. |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
175 PEAKachu uses signal and control libraries (ideally more than three each) to detect binding sites. |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
176 It implements two peak calling approaches |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
177 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
178 **adaptive** |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
179 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
180 The adaptive approach applies a three-step procedure to detect regions that are significantly enriched over controls. |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
181 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
182 - blockbuster is applied to the pooled libraries to combine similar sets of reads into blocks |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
183 - blocks are decomposed into peaks by iteratively applying a block merging heuristic |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
184 - peaks with significant enrichment of signal over control libraries are determined using DESeq2 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
185 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
186 **windowed** |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
187 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
188 The windowed approach subdivides the genome into overlapping regions. |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
189 After filtering of lowly expressed regions and library normalization (either using manual size factors, TMM, or DESeq2), this approach determines significantly enriched windows using eiterh DESeq2 or repeated G-tests of goodness-of-fit. |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
190 |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
191 ]]> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
192 </help> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
193 <citations> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
194 </citations> |
bc594df2aba3
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
rnateam
parents:
diff
changeset
|
195 </tool> |