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comparison pyCRAC/pyMotif.xml @ 0:19b20927172d draft

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author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
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1 <tool id ="pyMotif" name="pyMotif">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="perl">
6 pyMotif.pl
7 -f $input
8 --gtf=$addGTF.gtf
9
10 #if $addGTF.gtfFile == "default" and $addGTF.annotate.annotations == "auto":
11 --annotation $addGTF.annotate.scan.annotation
12 #else:
13 --annotation $addGTF.annotate.annotation
14 #end if#
15
16 --tab=$addTab.tab
17
18 #if $addOpt.options == "edit":
19 --options
20 --k_min $addOpt.kmin
21 --k_max $addOpt.kmax
22 --numberofkmers=$addOpt.numberofkmers
23 --overlap $addOpt.overlap
24 --range $addOpt.range
25 #end if#
26 -o "$input.name"
27 --id $count.id
28 --count $count
29 --random $random
30 --features $features
31 --zscores $zscores
32 </command>
33 <version_command>/usr/local/bin/pyMotif.py --version</version_command>
34 <inputs>
35 <param format="gtf" name="input" type="data" label="Input File --input_file" help="File of type .gtf" />
36 <conditional name="addTab">
37 <param name="tabFile" type="select" label="Choose Genomic Reference Sequence from">
38 <option value="default" selected="true">Defaults</option>
39 <option value="other">History</option>
40 </param>
41 <when value="default">
42 <param name="tab" type="select" label="Genomic Reference Sequence --tab" help="Tab file containing genomic reference sequence">
43 <options from_data_table="pycrac_tab"/>
44 </param>
45 </when>
46 <when value="other">
47 <param format="tabular" name="tab" type="data" label="Genomic Reference Sequence --tab" help="Tab file containing genomic reference sequence"/>
48 </when>
49 </conditional>
50 <conditional name="addGTF">
51 <param name="gtfFile" type="select" label="Choose GTF File from">
52 <option value="default" selected="true">Defaults</option>
53 <option value="other">History</option>
54 </param>
55 <when value="default">
56 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
57 <options from_data_table="pycrac_gtf"/>
58 </param>
59
60 <conditional name="annotate">
61 <param name="annotations" type="select" label="Select annotation">
62 <option value="all" selected="true">All</option>
63 <option value="manual">Enter in text box</option>
64 <option value="auto">Scan pyGetGTFSources file</option>
65 </param>
66 <when value="all">
67 <param name="annotation" type="hidden" format="txt" size="10" value="all"/>
68 </when>
69 <when value="manual">
70 <param name="annotation" type="text" format="txt" size="100" value="protein_coding" label="Select which annotation to focus search on --annotation" help="To find a list of available annotations please use pyGetGTFSources tool">
71 <validator type="empty_field" message="Please enter a value"/>
72 </param>
73 </when>
74 <when value="auto">
75 <param format="tabular" name="gtf_annotation" type="data" label="GTF annotation File (pyGetGTFSources output)" help="Tabular file containing unique list of annotations/sources in selected GTF file. Refer to pyGetGTFSources"/>
76 <conditional name="scan">
77 <param name="annotations" type="select" label="Scan this file for annotations" help="Choose the correct GTF file then choose GO">
78 <option value="wait" selected="true">Waiting</option>
79 <option value="scanning">Go</option>
80 </param>
81 <when value="wait">
82 </when>
83 <when value="scanning">
84 <param name="annotation" type="select" multiple="false" label="Select which annotation to focus search on --annotation">
85 <options from_dataset="gtf_annotation">
86 <column name="name" index="0"/>
87 <column name="value" index="0"/>
88 </options>
89 </param>
90 </when>
91 </conditional>
92 </when>
93 </conditional>
94 </when>
95 <when value="other">
96 <param format="gtf" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
97 <conditional name="annotate">
98 <param name="annotations" type="select" label="Select annotation">
99 <option value="all" selected="true">All</option>
100 <option value="manual">Enter in text box</option>
101 <option value="auto">Scan selected file</option>
102 </param>
103 <when value="all">
104 <param name="annotation" type="hidden" format="txt" size="10" value="all"/>
105 </when>
106 <when value="manual">
107 <param name="annotation" type="text" format="txt" size="100" value="protein_coding" label="Select which annotation to focus search on --annotation" help="To find a list of available annotations please use pyGetGTFSources tool">
108 <validator type="empty_field" message="Please enter a value"/>
109 </param>
110 </when>
111 <when value="auto">
112 <param name="annotation" type="select" multiple="false" label="Select which annotation to focus search on --annotation">
113 <options from_dataset="gtf">
114 <column name="name" index="1"/>
115 <column name="value" index="1"/>
116 <filter type="unique_value" name="unique" column="1"/>
117 </options>
118 </param>
119 </when>
120 </conditional>
121 </when>
122 </conditional>
123 <conditional name="addOpt">
124 <param name="options" type="select" label="Standard options">
125 <option value="default" selected="true">Default</option>
126 <option value="edit">Edit</option>
127 </param>
128 <when value="edit">
129 <param format="integer" name="kmin" type="integer" label="Minimum k-mer Length --k_min " value="4" size="6" help="Set the minimal k-mer length">
130 <validator type="in_range" min="1" message="Please enter a value >= 1"/>
131 </param>
132 <param format="integer" name="kmax" type="integer" label="Maximum k-mer Length --k_min " value="8" size="6" help="Set the minimal k-mer length">
133 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
134 </param>
135 <param format="integer" name="numberofkmers" type="integer" label="Maximum number of k-mers in output file --numberofkmers" value="1000" size="6" help="Set the maximum number of k-mers in output">
136 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
137 </param>
138 <param format="integer" name="range" type="integer" label="Range --range" value="0" size="5" help="Manually set the length of the 5' and 3' UTRs 0>50000">
139 <validator type="in_range" min="0" max="50000" message="Please enter a value between 0 and 50000"/>
140 </param>
141 <param format="integer" name="overlap" type="integer" label="Overlap --overlap" value="1" size="5" help="Sets the number of nucleotides a read has to overlap with a gene before it is considered a hit. ">
142 <validator type="in_range" min="1" message="Please enter a positive integer"/>
143 </param>
144 </when>
145 <when value="default">
146 </when>
147 </conditional>
148 <param name="label" type="text" format="txt" size="30" value="pyMotif" label="Enter output file label -o" />
149 </inputs>
150
151 <outputs>
152 <data format="tabular" name="zscores" label="${label.value}_k-mer_Z_scores.txt"/>
153 <data format="tabular" name="count" label="${label.value}_data_k-mers_count.txt"/>
154 <data format="gtf" name="features" label="${label.value}_top_k-mers_in_features.gtf"/>
155 <data format="tabular" name="random" label="${label.value}_random_k-mers_count.txt"/>
156 </outputs>
157 <help>
158
159 .. class:: infomark
160
161 **pyMotif**
162
163 pyMotif is part of the pyCRAC_ package. Looks for enriched sequence motifs in high-throughput sequencing data. Produces a GTF type output file
164 with coordinates and Z-scores for enriched motifs. The GTF file can be visualised in genome browsers.
165
166 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
167
168 ------
169
170 **Parameter list**
171
172 File input options::
173
174 -f intervals.gtf, --input_file=intervals.gtf
175 Provide the path to an interval gtf file. By default
176 it expects data from the standard input.
177 -o OUTPUT_FILE, --output_file=OUTPUT_FILE
178 Use this flag to override the standard file names. Do
179 NOT add an extension.
180 --gtf=annotation_file.gtf
181 type the path to the gtf annotation file that you want
182 to use
183 --tab=tab_file.tab
184 type the path to the tab file that contains the
185 genomic reference sequence
186
187 pyMotif specific options::
188
189 --k_min=4
190 this option allows you to set the shortest k-mer
191 length. Default = 4.
192 --k_max=6
193 this option allows you to set the longest k-mer
194 length. Default = 8.
195 -n 100, --numberofkmers=100
196 choose the maximum number of enriched k-mer sequences
197 you want to have reported in output files. Default =
198 1000
199
200 pyCRAC common options::
201
202 -a protein_coding, --annotation=protein_coding
203 select which annotation (i.e. protein_coding, ncRNA,
204 sRNA, rRNA,snoRNA,snRNA, depending on the source of
205 your GTF file) you would like to focus your search on.
206 Default = all annotations
207 -r 100, --range=100
208 allows you to add regions flanking the genomic
209 feature. If you set '-r 50' or '--range=50', then the
210 program will add 50 nucleotides to each feature on
211 each side regardless of whether the GTF file has genes
212 with annotated UTRs.
213 --overlap=1
214 sets the number of nucleotides a motif has to overlap
215 with a genomic feature before it is considered a hit.
216 Default = 1 nucleotide
217
218
219
220
221 </help>
222 </tool>