Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

annotate nucDyn_stats.xml @ 2:e88c806ddf3e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 05:28:43 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
1 <tool id="nucDyn_stats" name="Nucleosome Dynamics Statistics" version="0.1">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
2 <description>: statistics on Nucleosome Dynamics analysis</description>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
3 <requirements>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
4 <requirement type="binary">docker</requirement>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
5 </requirements>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
6 <command>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
7 <![CDATA[
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
8 ln -f -s $output_gw_png_file $output_gw_png_file\.png;
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
9 docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics nucDyn_stats --input $gff_file
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
10 #if $assembly.source == "buildin":
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
11 --genome ${assembly.ref_genome_gff_buildin}
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
12 #else if $assembly.source == "history":
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
13 --genome ${assembly.ref_genome_gff_history}
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
14 #end if
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
15 --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png;
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
16 rm $output_gw_png_file\.png
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
17 ]]>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
18 </command>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
19 <inputs>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
20 <param name="gff_file" type="data" format="gff" label="Nucleosome Architecture (GFF)" help="Annotation of nucleosome changes as produced by Nucleosome Dynamics"/>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
21 <conditional name="assembly">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
22 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
23 <option value="buildin" selected="True">Use a built-in genome</option>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
24 <option value="history">Use a genome from the history</option>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
25 </param>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
26 <when value="buildin">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
27 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
28 <options from_file="nucldyn_publicdata.loc">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
29 <column name="name" index="2"/>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
30 <column name="value" index="4"/>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
31 </options>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
32 </param>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
33 </when>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
34 <when value="history">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
35 <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
36 </when>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
37 </conditional>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
38 </inputs>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
39 <outputs>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
40 <data format="csv" name="output_genes_csv_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
41 <data format="png" name="output_gw_png_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" />
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
42 </outputs>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
43 <tests>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
44 <test>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
45 <param name="gff_file" value="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
46 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
47 <output name="output_genes_csv_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv" />
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
48 <output name="output_gw_png_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png" />
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
49 </test>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
50 </tests>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
51 <help>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
52 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
53 :height: 80
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
54 :width: 200
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
55
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
56 -----
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
57
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
58 Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them.
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
59
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
60 .. class:: infomark
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
61
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
62 Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
63 </help>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
64 <citations>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
65 <citation type="bibtex">
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
66 @misc{github,
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
67 author = {Buitrago D},
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
68 year = {2019},
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
69 title = {Nucleosome Dynamics suite: containerized installation},
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
70 publisher = {GitHub},
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
71 journal = {GitHub repository},
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
72 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
73 }</citation>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
74 </citations>
e88c806ddf3e Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
75 </tool>