Mercurial > repos > mvdbeek > damidseq_core

annotate damidseq_core.xml @ 6:9b13b8bda9d8 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/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
author mvdbeek
date Fri, 20 Apr 2018 06:14:00 -0400
parents 6c00620084a5
children 02f09108bcff
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
1 <tool id="damidseq_core" name="damidseq" version="0.1.4">
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
2 <description>align, extend and normalize a DamID-seq experiment</description>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
3 <requirements>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
4 <requirement type="package" version="1.4">damidseq_pipeline</requirement>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
5 </requirements>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
5
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
8 #set dam_file = 'A001.fastq.gz' if str($dam.ext).endswith('.gz') else 'A001.fastq'
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
9 #set dam_fusion_file = 'A002.fastq.gz' if str($dam_fusion.ext).endswith('.gz') else 'A002.fastq'
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
10 ln -f -s '$dam' $dam_file &&
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
11 ln -f -s '$dam_fusion' $dam_fusion_file &&
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
12 ln -f -s '$index' index.txt &&
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
13 HOME="\$PWD" damidseq_pipeline
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
14 --bins=$bins
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
15 --bowtie=1
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
16 --bowtie2_genome_dir='$reference_index.fields.path'
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
17 --extend_reads=$extend_reads
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
18 --extension_method='$extension_method'
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
19 $full_data_files
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
20 --gatc_frag_file='$gatc_frag_file'
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
21 --len=$len
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
22 --max_norm_value='$max_norm_value'
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
23 $method_subtract
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
24 --min_norm_value='$min_norm_value'
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
25 --norm_method=$norm_method
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
26 --norm_steps=$norm_steps
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
27 --output_format=$output_format
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
28 --q=$q
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
29 --qscore1max=$qscore1max
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
30 --qscore1min=$qscore1min
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
31 --qscore2max=$qscore2max
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
32 --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
33 mv Fusion-vs-Dam.gatc.* gatc.output
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
34 #if str($full_data_files):
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
35 && mv Fusion-vs-Dam.* full.output
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
36 #end if
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
37 ]]></command>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
38 <configfiles>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
39 <configfile name="index">A1 Dam
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
40 A2 Fusion</configfile>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
41 </configfiles>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
42 <inputs>
3
e47f77820200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit a76f114f428e08215ade1bd5cfebd86138243f75
mvdbeek
parents: 2
diff changeset
43 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
5
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
44 <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
45 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
46 <options from_data_table="bowtie2_indexes">
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
47 <filter type="sort_by" column="2"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
48 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
49 </options>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
50 </param>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
51 <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
52 <param name="output_format" type="select" label="Select the output format for the peaks">
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
53 <option value="bedgraph">Bed</option>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
54 <option value="gff">GFF</option>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
55 </param>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
56 <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
57 <param argument="--extension_method" type="select" label="Select the read extension method" help="Select Full to extend all reads or GATC to extend reads to --len or to the next GATC site, whichever is shorter. Using this option increases peak resolution (default).">
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
58 <option value="gatc">To nearest GATC site</option>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
59 <option value="full">Full</option>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
60 </param>
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
61 <param argument="--full_data_files" type="boolean" truevalue="--full_data_files" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
62 <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
63 <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
64 <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
65 <param argument="--max_norm_value" type="float" value="5.0" label="Maximum log2 value to limit normalisation search at"/>
3
e47f77820200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit a76f114f428e08215ade1bd5cfebd86138243f75
mvdbeek
parents: 2
diff changeset
66 <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract Dam control values from Dam-fusion values instead of using the log2 ratio?"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
67 <param argument="--norm_method" type="select" label="Select normalization method">
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
68 <option value="kde">kernel density estimation of log2 GATC fragment ratio (recommended)</option>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
69 <option value="rpm">readcounts per million reads (not recommended for most use cases)</option>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
70 </param>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
71 <param argument="--norm_steps" type="integer" min="1" value="300" label="Number of points in normalisation routine"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
72 <param argument="--q" type="integer" value="30" min="0" label="Cutoff average Q score for aligned reads"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
73 <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
74 <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/>
2
69e346fb52a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8b51049c08c770c52ff8444af736c8b85c99db5d
mvdbeek
parents: 1
diff changeset
75 <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
76 </inputs>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
77 <outputs>
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
78 <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}">
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
79 <change_format>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
80 <when input="output_format" value="gff" format="gff" />
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
81 </change_format>
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
82 <actions>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
83 <action type="metadata" name="dbkey">
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
84 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
85 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
86 <filter type="param_value" ref="reference_index" column="0"/>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
87 </option>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
88 </action>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
89 </actions>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
90 </data>
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
91 <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}">
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
92 <filter>full_data_files == '--full_data_files'</filter>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
93 <change_format>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
94 <when input="output_format" value="gff" format="gff" />
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
95 </change_format>
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
96 <actions>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
97 <action type="metadata" name="dbkey">
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
98 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
99 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
100 <filter type="param_value" ref="reference_index" column="0"/>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
101 </option>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
102 </action>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
103 </actions>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
104 </data>
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
105 <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment on ${on_string}">
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
106 <actions>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
107 <action type="metadata" name="dbkey">
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
108 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
109 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
110 <filter type="param_value" ref="reference_index" column="0"/>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
111 </option>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
112 </action>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
113 </actions>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
114 </data>
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
115 <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment on ${on_string}">
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
116 <actions>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
117 <action type="metadata" name="dbkey">
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
118 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
119 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
120 <filter type="param_value" ref="reference_index" column="0"/>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
121 </option>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
122 </action>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
123 </actions>
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
124 </data>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
125 </outputs>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
126 <tests>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
127 <test>
5
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
128 <param name="dam" value="A001.fastq.gz"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
129 <param name="dam_fusion" value="A002.fastq.gz"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
130 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
131 <param name="reference_index" value="dm6"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
132 <param name="norm_method" value="rpm"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
133 <output name="output_ratio" file="output_ratio.bed"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
134 <output name="control_output" file="control.bam"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
135 <output name="fusion_output" file="fusion.bam"/>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
136 </test>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
137 <test>
6c00620084a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
mvdbeek
parents: 4
diff changeset
138 <param name="dam" value="A001.fastq"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
139 <param name="dam_fusion" value="A002.fastq"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
140 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
141 <param name="reference_index" value="dm6"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
142 <param name="norm_method" value="rpm"/>
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
143 <param name="full_data_files" value="true"/>
1
0d1514ecd757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
mvdbeek
parents: 0
diff changeset
144 <output name="output_ratio" file="output_ratio.bed"/>
6
9b13b8bda9d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
mvdbeek
parents: 5
diff changeset
145 <output name="output_ratio_full" file="output_ratio_full.bed"/>
0
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
146 <output name="control_output" file="control.bam"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
147 <output name="fusion_output" file="fusion.bam"/>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
148 </test>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
149 </tests>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
150 <help><![CDATA[
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
151
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
152 Processing DamID-seq data involves extending single-end reads, aligning
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
153 the reads to the genome and determining the coverage, similar to
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
154 processing regular ChIP-seq datasets. However, as DamID data is
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
155 represented as a log2 ratio of (Dam-fusion/Dam), normalisation of the
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
156 sample and Dam-only control is necessary and adding pseudocounts to
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
157 mitigate the effect of background counts is highly recommended.
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
158
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
159 damidseq_pipeline is a single script that automatically handles
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
160 sequence alignment, read extension, binned counts, normalisation,
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
161 pseudocount addition and final ratio file generation. The script uses
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
162 FASTQ or BAM files as input, and outputs the final log2 ratio files in
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
163 bedGraph (or optionally GFF) format.
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
164
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
165 The output ratio files can easily be converted to TDF for viewing in IGV using
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
166 igvtools. The files can be processed for peak calling using find_peaks or, if
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
167 using RNA pol II DamID, transcribed genes can be determined using
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
168 polii.gene.call.
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
169
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
170 ]]></help>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
171 <citations>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
172 <citation type="doi">10.1093/bioinformatics/btv386</citation>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
173 </citations>
eb3a145c4962 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit b'33637968e1e32c02d7765a6701e930a0ea0dd903\n'
mvdbeek
parents:
diff changeset
174 </tool>