Mercurial > repos > pjbriggs > macs21
annotate macs21_wrapper.xml @ 1:d0986d2be693 draft
Substantial reimplementation of internals, also renamed id and version.
| author | pjbriggs |
|---|---|
| date | Thu, 29 Jan 2015 11:11:21 -0500 |
| parents | fdad0c8c0957 |
| children | 15889783e759 |
| rev | line source |
|---|---|
|
1
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-1"> |
| 0 | 2 <requirements> |
| 3 <requirement type="package" version="2.7">python</requirement> | |
| 4 <requirement type="package" version="1.8.1">numpy</requirement> | |
| 5 <requirement type="package" version="2.1.0.20140616">macs2</requirement> | |
| 6 </requirements> | |
|
1
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
7 <description>Model-based Analysis of ChIP-Seq</description> |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
8 <command interpreter="python"> |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
9 macs21_wrapper.py |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
10 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
11 ## Major command |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
12 $major_command.major_command_selector |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
13 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
14 ## ChIP-seq input |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
15 $major_command.input_chipseq_file1 |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
16 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
17 ## ChIP-seq control |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
18 #if str($major_command.input_control_file1) != 'None' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
19 -c $major_command.input_control_file1 |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
20 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
21 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
22 ## Call peaks |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
23 #if str($major_command.major_command_selector) == 'callpeak' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
24 --format=$major_command.input_chipseq_file1.extension |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
25 --name="$experiment_name" |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
26 --bw=$major_command.bw |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
27 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
28 ## Genome size |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
29 #if str($major_command.genome_size.gsize) == '' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
30 --gsize=$major_command.genome_size.user_defined_gsize |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
31 #else: |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
32 --gsize=$major_command.genome_size.gsize |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
33 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
34 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
35 ## Broad peaks |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
36 #if str($major_command.broad_options.broad_regions) == 'broad' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
37 --broad --broad-cutoff=$major_command.broad_options.broad_cutoff |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
38 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
39 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
40 ## (no)model options |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
41 #if str($major_command.nomodel_type.nomodel_type_selector) == 'nomodel' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
42 --nomodel --extsize=$major_command.nomodel_type.extsize |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
43 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
44 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
45 ## pq value select options |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
46 #if str($major_command.pq_options.pq_options_selector) == 'qvalue' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
47 --qvalue=$major_command.pq_options.qvalue |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
48 #else |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
49 --pvalue=$major_command.pq_options.pvalue |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
50 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
51 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
52 ## Advanced options |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
53 #if str($major_command.advanced_options.advanced_options_selector) == 'on' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
54 --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
55 $major_command.advanced_options.nolambda |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
56 #if $major_command.bdg_options.bdg == True |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
57 -B $major_command.bdg_options.spmr |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
58 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
59 $major_command.advanced_options.call_summits |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
60 #if str($major_command.advanced_options.keep_duplicates.keep_dup) == '' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
61 --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
62 #else |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
63 --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
64 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
65 #else |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
66 ## Defaults if advanced options not set |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
67 --mfold 5 50 --keep-dup 1 |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
68 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
69 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
70 ## Output files |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
71 --output-summits=$output_summits_bed_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
72 --output-extra-files=$output_extra_files |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
73 --output-extra-files-path=$output_extra_files.files_path |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
74 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
75 ## Narrow/broad peak outputs |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
76 #if str($major_command.broad_options.broad_regions) == 'broad' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
77 --output-broadpeaks=$output_broadpeaks_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
78 --output-gappedpeaks=$output_gappedpeaks_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
79 #else |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
80 --output-narrowpeaks=$output_narrowpeaks_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
81 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
82 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
83 ## Bedgraph outputs |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
84 #if str($major_command.bdg_options.bdg) == 'True' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
85 --output-pileup $output_treat_pileup_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
86 --output-lambda-bedgraph=$output_lambda_bedgraph_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
87 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
88 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
89 ## XLS/interval output |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
90 #if str($major_command.xls_to_interval) == 'True' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
91 --output-xls-to-interval=$output_xls_to_interval_peaks_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
92 #else |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
93 --output-peaks=$output_peaks_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
94 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
95 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
96 ## |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
97 ## Compare .bdg files |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
98 #if str($major_command.major_command_selector) == 'bdgcmp' |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
99 -m $major_command.bdgcmp_options.bdgcmp_options_selector |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
100 -p $major_command.pseudocount |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
101 --output-bdgcmp $output_bdgcmp_file |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
102 #end if |
|
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
103 </command> |
| 0 | 104 <inputs> |
|
1
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
105 <!--experiment name used as base for output file names --> |
| 0 | 106 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" |
| 107 label="Experiment Name"/> | |
|
1
d0986d2be693
Substantial reimplementation of internals, also renamed id and version.
pjbriggs
parents:
0
diff
changeset
|
108 <!--select a major MACS2 command--> |
| 0 | 109 <conditional name="major_command"> |
| 110 <param name="major_command_selector" type="select" label="Select action to be performed"> | |
| 111 <option value="callpeak">Peak Calling</option> | |
| 112 <option value="bdgcmp">Compare .bdg Files</option> | |
| 113 </param> | |
| 114 <!--callpeak option of macs2--> | |
| 115 <when value="callpeak"> | |
| 116 <!--choose 'broad' or 'narrow' regions--> | |
| 117 <conditional name="broad_options"> | |
| 118 <param name="broad_regions" type="select" label="Type of region to call" | |
| 119 help="Broad regions are formed by linking nearby enriched regions"> | |
| 120 <option value="" selected="true">Narrow regions</option> | |
| 121 <option value="broad">Broad regions</option> | |
| 122 </param> | |
| 123 <when value="broad"> | |
| 124 <param name="broad_cutoff" type="float" | |
| 125 label="Cutoff for broad regions" | |
| 126 value="0.1" help="default: 0.1 (--broad-cutoff)"/> | |
| 127 </when> | |
| 128 </conditional> | |
| 129 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" | |
| 130 label="ChIP-seq read file" /> | |
| 131 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" | |
| 132 label="ChIP-seq control read file" /> | |
| 133 <conditional name="genome_size"> | |
| 134 <param name="gsize" type="select" label="Effective genome size" | |
| 135 help="Either pre-defined (for common organisms), or user-defined (--gsize)"> | |
| 136 <option value="hs" selected="true">Human (2.7e9)</option> | |
| 137 <option value="mm">Mouse (1.87e9)</option> | |
| 138 <option value="ce">C. elegans (9e7)</option> | |
| 139 <option value="dm">Fruitfly (1.2e8)</option> | |
| 140 <option value="">User-defined</option> | |
| 141 </param> | |
| 142 <when value=""> | |
| 143 <!-- User-defined effective genome size --> | |
| 144 <param name="user_defined_gsize" type="float" value="" | |
| 145 label="Enter effective genome size (number of bases)" | |
| 146 help="e.g. '1.0e+9' or '1000000000'" /> | |
| 147 </when> | |
| 148 </conditional> | |
| 149 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> | |
| 150 <param name="xls_to_interval" label="Include XLS file from MACS" | |
| 151 type="boolean" truevalue="True" falsevalue="False" checked="True" | |
| 152 help="MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based."/> | |
| 153 | |
| 154 <conditional name="bdg_options"> | |
| 155 <param name="bdg" | |
| 156 label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" | |
| 157 type="boolean" truevalue="-B" falsevalue="" checked="False" /> | |
| 158 <when value="-B"> | |
| 159 <param name="spmr" | |
| 160 type="boolean" truevalue="--SPMR" falsevalue="" checked="False" | |
| 161 label="Save signal per million reads for fragment pileup profiles" | |
| 162 help="(--SPMR)" /> | |
| 163 </when> | |
| 164 <when value=""> | |
| 165 <!-- Display nothing --> | |
| 166 </when> | |
| 167 </conditional> | |
| 168 | |
| 169 <conditional name="pq_options"> | |
| 170 <param name="pq_options_selector" type="select" | |
| 171 label="Select p-value or q-value" help="default uses q-value"> | |
| 172 <option value="qvalue">q-value</option> | |
| 173 <option value="pvalue">p-value</option> | |
| 174 </param> | |
| 175 <when value="pvalue"> | |
| 176 <param name="pvalue" type="float" | |
| 177 label="p-value cutoff for binding region detection" | |
| 178 value="1e-2" help="default: 1e-2 (--pvalue)"/> | |
| 179 </when> | |
| 180 <when value="qvalue"> | |
| 181 <param name="qvalue" type="float" | |
| 182 label="q-value cutoff for binding region detection" | |
| 183 value="0.01" help="default: 0.01 (--qvalue)"/> | |
| 184 </when> | |
| 185 </conditional> | |
| 186 <conditional name="advanced_options"> | |
| 187 <param name="advanced_options_selector" type="select" | |
| 188 label="Display advanced options"> | |
| 189 <option value="off">Hide</option> | |
| 190 <option value="on">Display</option> | |
| 191 </param> | |
| 192 <when value="on"> | |
| 193 <param name="mfoldlo" type="integer" | |
| 194 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" | |
| 195 value="10" help="(--mfold)"/> | |
| 196 <param name="mfoldhi" type="integer" | |
| 197 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" | |
| 198 value="30" help="(--mfold)"/> | |
| 199 <param name="nolambda" | |
| 200 label="Use fixed background lambda as local lambda for every binding region" | |
| 201 type="boolean" truevalue="--nolambda" falsevalue="" checked="False" | |
| 202 help="(--nolambda)"/> | |
| 203 <param name="call_summits" | |
| 204 label="Detect subpeaks within binding region" | |
| 205 type="boolean" truevalue="--call-summits" falsevalue="" checked="False" | |
| 206 help="(--call-summits)"/> | |
| 207 <conditional name="keep_duplicates"> | |
| 208 <param name="keep_dup" type="select" | |
| 209 label="Use of duplicate reads"> | |
| 210 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option> | |
| 211 <option value="all">Use all duplicates (all)</option> | |
| 212 <option value="" selected="true">Manually specify maxium number of duplicates</option> | |
| 213 </param> | |
| 214 <when value=""> | |
| 215 <param name="maximum_tags" type="integer" value="1" | |
| 216 label="Maxium number of duplicated tags to keep at each location"/> | |
| 217 </when> | |
| 218 </conditional> | |
| 219 </when> | |
| 220 <when value="off"> | |
| 221 <!--display nothing--> | |
| 222 </when> | |
| 223 </conditional> | |
| 224 <conditional name="nomodel_type"> | |
| 225 <param name="nomodel_type_selector" type="select" label="Build Model"> | |
| 226 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> | |
| 227 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> | |
| 228 </param> | |
| 229 <when value="nomodel"> | |
| 230 <param name="extsize" type="integer" label="Arbitrary extension size in bp" value="200" help="Used as fragment size to extend each read towards 3' end (--extsize)"/> | |
| 231 </when> | |
| 232 </conditional> | |
| 233 </when> | |
| 234 | |
| 235 <!--callpeak option of macs2--> | |
| 236 <when value="bdgcmp"> | |
| 237 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" | |
| 238 label="ChIP-seq read file" /> | |
| 239 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" | |
| 240 label="ChIP-seq control read file" /> | |
| 241 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" | |
| 242 help="default: 0.00001 (-p)"/> | |
| 243 <conditional name="bdgcmp_options"> | |
| 244 <param name="bdgcmp_options_selector" type="select" | |
| 245 label="Select action to be performed"> | |
| 246 <option value="ppois">ppois</option> | |
| 247 <option value="qpois">qpois</option> | |
| 248 <option value="subtract">subtract</option> | |
| 249 <option value="logFE">logFE</option> | |
| 250 <option value="FE">FE</option> | |
| 251 <option value="logLR">logLR</option> | |
| 252 </param> | |
| 253 </conditional> | |
| 254 </when> | |
| 255 </conditional> | |
| 256 </inputs> | |
| 257 | |
| 258 <outputs> | |
| 259 <!--callpeaks output--> | |
| 260 <data name="output_extra_files" format="html" | |
| 261 label="${tool.name}: callpeak on ${on_string} (html report)"> | |
| 262 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 263 </data> | |
| 264 <data name="output_summits_bed_file" format="bed" | |
| 265 label="${tool.name}: callpeak on ${on_string} (summits: bed)"> | |
| 266 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 267 </data> | |
| 268 <data name="output_peaks_file" format="xls" | |
| 269 label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> | |
| 270 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 271 <filter>major_command['xls_to_interval'] is False</filter> | |
| 272 </data> | |
| 273 <data name="output_narrowpeaks_file" format="interval" | |
| 274 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)"> | |
| 275 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 276 <filter>major_command['broad_options']['broad_regions'] == ''</filter> | |
| 277 </data> | |
| 278 <data name="output_broadpeaks_file" format="interval" | |
| 279 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)"> | |
| 280 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 281 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter> | |
| 282 </data> | |
| 283 <data name="output_gappedpeaks_file" format="interval" | |
| 284 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)"> | |
| 285 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 286 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter> | |
| 287 </data> | |
| 288 <data name="output_xls_to_interval_peaks_file" format="interval" | |
| 289 label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> | |
| 290 <filter>major_command['xls_to_interval'] is True</filter> | |
| 291 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 292 </data> | |
| 293 <data name="output_treat_pileup_file" format="bedgraph" | |
| 294 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)"> | |
| 295 <filter>major_command['bdg_options']['bdg'] is True</filter> | |
| 296 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 297 </data> | |
| 298 <data name="output_lambda_bedgraph_file" format="bedgraph" | |
| 299 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> | |
| 300 <filter>major_command['bdg_options']['bdg'] is True</filter> | |
| 301 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 302 </data> | |
| 303 <!--bdgcmp output--> | |
| 304 <data name="output_bdgcmp_file" format="bdg" | |
| 305 label="${tool.name}: bdgcmp on ${on_string} (bdg)"> | |
| 306 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter> | |
| 307 </data> | |
| 308 </outputs> | |
| 309 <tests> | |
| 310 <!--none yet for macs2--> | |
| 311 </tests> | |
| 312 <help> | |
| 313 | |
| 314 .. class:: warningmark | |
| 315 | |
| 316 **This is a modified version of the standard Galaxy toolshed "MACS2" tool, | |
| 317 which has been customised for users at the University of Manchester to work | |
| 318 with MACS 2.1.0.** | |
| 319 | |
| 320 It is based on the 16:14f378e35191 revision of the tool at | |
| 321 | |
| 322 * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 | |
| 323 | |
| 324 ------ | |
| 325 | |
| 326 **What it does** | |
| 327 | |
| 328 With the improvement of sequencing techniques, chromatin immunoprecipitation | |
| 329 followed by high throughput sequencing (ChIP-Seq) is getting popular to study | |
| 330 genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq | |
| 331 analysis method, we present a novel algorithm, named Model-based Analysis of | |
| 332 ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures | |
| 333 the influence of genome complexity to evaluate the significance of enriched | |
| 334 ChIP regions, and MACS improves the spatial resolution of binding sites through | |
| 335 combining the information of both sequencing tag position and orientation. MACS | |
| 336 can be easily used for ChIP-Seq data alone, or with control sample with the | |
| 337 increase of specificity. | |
| 338 | |
| 339 View the original MACS2 documentation: | |
| 340 https://github.com/taoliu/MACS/blob/master/README.rst | |
| 341 | |
| 342 ------ | |
| 343 | |
| 344 **Usage** | |
| 345 | |
| 346 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results. | |
| 347 | |
| 348 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. | |
| 349 | |
| 350 | |
| 351 ------ | |
| 352 | |
| 353 **Citation** | |
| 354 | |
| 355 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. | |
| 356 | |
| 357 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. | |
| 358 </help> | |
| 359 </tool> |