Mercurial > repos > rnateam > footprint
comparison footprint.xml @ 1:0d94a529f925 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author | rnateam |
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date | Mon, 20 Nov 2017 05:04:27 -0500 |
parents | 4bff424dfa47 |
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0:4bff424dfa47 | 1:0d94a529f925 |
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1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
2 <tool id="footprint" name="footprint" version="1.0.0"> | 2 <tool id="footprint" name="footprint" version="1.0.0"> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.0.0">footprint</requirement> | 4 <requirement type="package" version="1.0.0">footprint</requirement> |
5 </requirements> | 5 </requirements> |
6 <stdio> | 6 <command detect_errors="aggressive"><![CDATA[ |
7 <exit_code range="1:" /> | 7 ln -s '$bam_file' ./bam_file.bam |
8 </stdio> | 8 && |
9 <command><![CDATA[ | 9 find_footprints.sh |
10 ln -s '$bam_file' ./bam_file.bam | 10 ./bam_file.bam |
11 '$chrom_sizes' | |
12 '$motif_coords' | |
13 ## genome source | |
14 #if $refGenomeSource.genomeSource == "history": | |
15 '$refGenomeSource.ownFile' | |
16 #else | |
17 '$refGenomeSource.builtin.fields.path' | |
18 #end if | |
19 '$factor_name' | |
20 '$bias_file' | |
21 '$peak_file' | |
22 $no_of_components | |
23 $background | |
24 $fixed_bg | |
25 && | |
26 mv *.PARAM PARAM && | |
27 mv *.RESULTS RESULTS && | |
28 mv *.plot2.png plot2.png && | |
29 mv *.plot1.png plot1.png | |
11 | 30 |
12 && | |
13 | |
14 find_footprints.sh | |
15 | |
16 ./bam_file.bam | |
17 | |
18 '$chrom_sizes' | |
19 | |
20 '$motif_coords' | |
21 | |
22 ## genome source | |
23 #if $refGenomeSource.genomeSource == "history": | |
24 '$refGenomeSource.ownFile' | |
25 #else | |
26 '$refGenomeSource.builtin.fields.path' | |
27 #end if | |
28 | |
29 $factor_name | |
30 | |
31 '$bias_file' | |
32 | |
33 '$peak_file' | |
34 | |
35 $no_of_components | |
36 | |
37 $background | |
38 | |
39 $fixed_bg | |
40 | |
41 && | |
42 mv *.PARAM PARAM | |
43 && | |
44 mv *.RESULTS RESULTS | |
45 && | |
46 mv *.plot2.png plot2.png | |
47 && | |
48 mv *.plot1.png plot1.png | |
49 ]]> | 31 ]]> |
50 </command> | 32 </command> |
51 <inputs> | 33 <inputs> |
52 <param name="bam_file" type="data" format="BAM" label="alignment bam file" help="" /> | 34 <param name="bam_file" type="data" format="BAM" label="alignment bam file" help="" /> |
53 <param name="chrom_sizes" type="data" format="tablular" label="chromosome length" help="" /> | 35 <param name="chrom_sizes" type="data" format="tablular" label="chromosome length" help="" /> |
123 | 105 |
124 **Purpose** | 106 **Purpose** |
125 | 107 |
126 This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data. | 108 This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data. |
127 | 109 |
128 | |
129 ----- | 110 ----- |
130 | 111 |
131 .. class:: infomark | 112 .. class:: infomark |
132 | 113 |
133 **Inputs** | 114 **Inputs** |
142 | 123 |
143 coordinates of motif | 124 coordinates of motif |
144 * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest. | 125 * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest. |
145 * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based). | 126 * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based). |
146 * Example: chr1 24782 24800 . 11.60 - | 127 * Example: chr1 24782 24800 . 11.60 - |
128 * There should not be any additional columns. | |
147 | 129 |
148 transcription factor | 130 transcription factor |
149 * The name of the transcription factor of interest supplied by the user, e.g. CTCF. | 131 * The name of the transcription factor of interest supplied by the user, e.g. CTCF. |
150 | 132 |
151 cleavage/transposition bias | 133 cleavage/transposition bias |
170 | 152 |
171 fixed background component | 153 fixed background component |
172 * Whether the background component should be kept fixed. | 154 * Whether the background component should be kept fixed. |
173 * Options are TRUE or FALSE. | 155 * Options are TRUE or FALSE. |
174 * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training. | 156 * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training. |
157 * In general, if the background is estimated from bias (option "Seq"), it is recommended to keep it fixed. | |
175 | 158 |
176 ----- | 159 ----- |
177 | 160 |
178 .. class:: infomark | 161 .. class:: infomark |
179 | 162 |
199 * When 3 components are used, this plot shows the weighted average of the 2 footprint components as the final footprint profile. | 182 * When 3 components are used, this plot shows the weighted average of the 2 footprint components as the final footprint profile. |
200 | 183 |
201 ]]></help> | 184 ]]></help> |
202 <citations> | 185 <citations> |
203 <citation type="bibtex">@ARTICLE{footprint, | 186 <citation type="bibtex">@ARTICLE{footprint, |
204 author = {Aslihan Karabacak and Uwe Ohler}, | 187 author = {Aslihan Karabacak, Galip Gurkan Yardimci, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler}, |
205 title = {To submit}, | 188 title = {To submit}, |
206 journal = {}, | 189 journal = {}, |
207 year = {}, | 190 year = {}, |
208 volume = {}, | 191 volume = {}, |
209 pages = {} | 192 pages = {} |