Mercurial > repos > iuc > homer_annotatepeaks

annotate homer_annotatePeaks.xml @ 2:35dc2f57d755 draft

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/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
author iuc
date Mon, 13 Dec 2021 15:16:02 +0000
parents adab852c8216
children fa7c3a74acf2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1 <tool id="homer_annotatePeaks" name="annotatePeaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
2 <macros>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
3 <import>macros.xml</import>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
4 </macros>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
5 <expand macro="requirements"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
7 annotatePeaks.pl
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
8 ## Peak file
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
9 '$input'
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
10 ## Genome
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
11 #if $CpG.bool == "true":
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
12 #if $CpG.genome.source == 'installed':
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
13 '${CpG.genome.all_fasta_source.fields.path}'
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
14 #else
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
15 '${CpG.genome.fasta}'
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
16 #end if
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
17 -CpG
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
18 #else
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
19 none
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
20 #end if
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
21 #if $gtf_file:
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
22 -gtf '$gtf_file'
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
23 #end if
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
24 #if $ann_file:
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
25 -ann '$ann_file'
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
26 #end if
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
27 > '$output'
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
28 ]]></command>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
29 <inputs>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
30 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
31 <!-- CpG -->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
32 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
33 <param name="bool" type="select" label="Do you want to compute CpG/GC content?">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
34 <option value="true">Yes</option>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
35 <option value="false">No</option>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
36 </param>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
37 <when value="true">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
38 <conditional name="genome">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
39 <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
40 <option value="installed">Installed</option>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
41 <option value="history">From History</option>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
42 </param>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
43 <when value="installed">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
44 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
45 <options from_data_table="all_fasta">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
46 <filter type="sort_by" column="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
47 <validator type="no_options" message="No references are available"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
48 </options>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
49 </param>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
50 </when>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
51 <when value="history">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
52 <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
53 </when>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
54 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
55 </when>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
56 <when value="false"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
57 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
58 <param name="gtf_file" type="data" format="gtf,gff,gff3" optional="True" label="GTF file" help="Must be of datatype &quot;gtf&quot; or &quot;gff&quot; or &quot;gff3&quot;" argument="-gtf"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
59 <param name="ann_file" type="data" format="tabular" optional="True" label="Annotation data file for HOMER" help="This file can be generated from gtf with the tool 'Converts GTF to Annotations file for Homer" argument="-ann"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
60 </inputs>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
61 <outputs>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
62 <data format="tabular" name="output"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
63 </outputs>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
64 <tests>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
65 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
66 <!-- first simple test with ann and gtf-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
67 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
68 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
69 <param name="bool" value="false"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
70 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
71 <param name="ann_file" value="annotations_default_simplified.txt" ftype="tabular"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
72 <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
73 <output name="output" file="CTCF_peaks_first.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
74 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
75 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
76 <!-- second simple test with ann only-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
77 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
78 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
79 <param name="bool" value="false"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
80 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
81 <param name="ann_file" value="annotations_default.txt" ftype="tabular"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
82 <output name="output" file="CTCF_peaks_second.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
83 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
84 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
85 <!-- third simple test with gtf only-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
86 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
87 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
88 <param name="bool" value="false"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
89 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
90 <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
91 <output name="output" file="CTCF_peaks_third.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
92 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
93 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
94 <!--test with CpG-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
95 <param name="input" value="fake_phix_peaks.bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
96 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
97 <param name="bool" value="true"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
98 <conditional name="genome">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
99 <param name="source" value="history"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
100 <param name="fasta" value="phiX174.fasta"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
101 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
102 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
103 <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
104 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
105 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
106 <!--test with CpG from table-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
107 <param name="input" value="fake_phix_peaks.bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
108 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
109 <param name="bool" value="true"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
110 <conditional name="genome">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
111 <param name="source" value="installed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
112 <param name="all_fasta_source" value="phiX174"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
113 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
114 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
115 <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
116 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
117 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
118 <!--test with nothing-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
119 <param name="input" value="fake_phix_peaks.bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
120 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
121 <param name="bool" value="false"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
122 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
123 <output name="output" file="phiX_nothing.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
124 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
125 </tests>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
126 <help><![CDATA[
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
127 This wrapper allow to annotate peaks with simple annotations with annotatePeaks.pl from HOMER.
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
128 The annotation file and the GTF file may seem redundant but:
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
129 - the use of gtf file only misses the UTR annotations and does not allow to set the desired offsets for TSS and TTS.
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
130 - the use of annotation file only misses the distance to tss and the correspondance between id and classical gene name.
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
131 ]]></help>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
132 <expand macro="citation"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
133 </tool>