Mercurial > repos > iuc > homer_annotatepeaks

comparison homer_annotatePeaks.xml @ 0:adab852c8216 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
author iuc
date Sun, 08 Aug 2021 11:03:29 +0000
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children fa7c3a74acf2
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-1:000000000000 0:adab852c8216
1 <tool id="homer_annotatePeaks" name="annotatePeaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[
7 annotatePeaks.pl
8 ## Peak file
9 '$input'
10 ## Genome
11 #if $CpG.bool == "true":
12 #if $CpG.genome.source == 'installed':
13 '${CpG.genome.all_fasta_source.fields.path}'
14 #else
15 '${CpG.genome.fasta}'
16 #end if
17 -CpG
18 #else
19 none
20 #end if
21 #if $gtf_file:
22 -gtf '$gtf_file'
23 #end if
24 #if $ann_file:
25 -ann '$ann_file'
26 #end if
27 > '$output'
28 ]]></command>
29 <inputs>
30 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/>
31 <!-- CpG -->
32 <conditional name="CpG">
33 <param name="bool" type="select" label="Do you want to compute CpG/GC content?">
34 <option value="true">Yes</option>
35 <option value="false">No</option>
36 </param>
37 <when value="true">
38 <conditional name="genome">
39 <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
40 <option value="installed">Installed</option>
41 <option value="history">From History</option>
42 </param>
43 <when value="installed">
44 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
45 <options from_data_table="all_fasta">
46 <filter type="sort_by" column="2"/>
47 <validator type="no_options" message="No references are available"/>
48 </options>
49 </param>
50 </when>
51 <when value="history">
52 <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
53 </when>
54 </conditional>
55 </when>
56 <when value="false"/>
57 </conditional>
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"/>
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"/>
60 </inputs>
61 <outputs>
62 <data format="tabular" name="output"/>
63 </outputs>
64 <tests>
65 <test expect_num_outputs="1">
66 <!-- first simple test with ann and gtf-->
67 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
68 <conditional name="CpG">
69 <param name="bool" value="false"/>
70 </conditional>
71 <param name="ann_file" value="annotations_default_simplified.txt" ftype="tabular"/>
72 <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/>
73 <output name="output" file="CTCF_peaks_first.txt" ftype="tabular" compare="diff" lines_diff="2"/>
74 </test>
75 <test expect_num_outputs="1">
76 <!-- second simple test with ann only-->
77 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
78 <conditional name="CpG">
79 <param name="bool" value="false"/>
80 </conditional>
81 <param name="ann_file" value="annotations_default.txt" ftype="tabular"/>
82 <output name="output" file="CTCF_peaks_second.txt" ftype="tabular" compare="diff" lines_diff="2"/>
83 </test>
84 <test expect_num_outputs="1">
85 <!-- third simple test with gtf only-->
86 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
87 <conditional name="CpG">
88 <param name="bool" value="false"/>
89 </conditional>
90 <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/>
91 <output name="output" file="CTCF_peaks_third.txt" ftype="tabular" compare="diff" lines_diff="2"/>
92 </test>
93 <test expect_num_outputs="1">
94 <!--test with CpG-->
95 <param name="input" value="fake_phix_peaks.bed"/>
96 <conditional name="CpG">
97 <param name="bool" value="true"/>
98 <conditional name="genome">
99 <param name="source" value="history"/>
100 <param name="fasta" value="phiX174.fasta"/>
101 </conditional>
102 </conditional>
103 <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/>
104 </test>
105 <test expect_num_outputs="1">
106 <!--test with CpG from table-->
107 <param name="input" value="fake_phix_peaks.bed"/>
108 <conditional name="CpG">
109 <param name="bool" value="true"/>
110 <conditional name="genome">
111 <param name="source" value="installed"/>
112 <param name="all_fasta_source" value="phiX174"/>
113 </conditional>
114 </conditional>
115 <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/>
116 </test>
117 <test expect_num_outputs="1">
118 <!--test with nothing-->
119 <param name="input" value="fake_phix_peaks.bed"/>
120 <conditional name="CpG">
121 <param name="bool" value="false"/>
122 </conditional>
123 <output name="output" file="phiX_nothing.txt" ftype="tabular" compare="diff" lines_diff="2"/>
124 </test>
125 </tests>
126 <help><![CDATA[
127 This wrapper allow to annotate peaks with simple annotations with annotatePeaks.pl from HOMER.
128 The annotation file and the GTF file may seem redundant but:
129 - the use of gtf file only misses the UTR annotations and does not allow to set the desired offsets for TSS and TTS.
130 - the use of annotation file only misses the distance to tss and the correspondance between id and classical gene name.
131 ]]></help>
132 <expand macro="citation"/>
133 </tool>