0
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
1 <tool id="nucDyn_stats" name="Nucleosome Dynamics Statistics" version="0.1">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
2 <description>: statistics on Nucleosome Dynamics analysis</description>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
3 <requirements>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
4 <requirement type="binary">docker</requirement>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
5 </requirements>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
6 <command>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
7 <![CDATA[
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
8 ln -f -s $output_gw_png_file $output_gw_png_file\.png;
|
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/nucldyn nucDyn_stats --input $gff_file
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
10 #if $assembly.source == "buildin":
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
11 --genome ${assembly.ref_genome_gff_buildin}
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
12 #else if $assembly.source == "history":
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
13 --genome ${assembly.ref_genome_gff_history}
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
14 #end if
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
15 --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png;
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
16 rm $output_gw_png_file\.png
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
17 ]]>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
18 </command>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
19 <inputs>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
20 <param name="gff_file" type="data" format="gff" label="Input Nucleosome Calls"/>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
21 <conditional name="assembly">
|
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 chromosome sizes and their annotated genes.">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
23 <option value="buildin" selected="True">Use a built-in genome</option>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
24 <option value="history">Use a genome from the history</option>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
25 </param>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
26 <when value="buildin">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
27 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
28 <options from_file="nucldyn_publicdata.loc">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
29 <column name="name" index="2"/>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
30 <column name="value" index="4"/>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
31 </options>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
32 </param>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
33 </when>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
34 <when value="history">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
35 <param name="ref_genome_gff_history" type="data" format="gff" label="Select gene annotations for your reference genome" help="Check below the documentation for lerning about the file format."/>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
36 </when>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
37 </conditional>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
38 </inputs>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
39 <outputs>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
40 <data format="csv" name="output_genes_csv_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
41 <data format="png" name="output_gw_png_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" />
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
42 </outputs>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
43 <tests>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
44 <test>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
45 <param name="gff_file" value="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" />
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
46 <param name="ref_genome_gff_buildin" value="genes.gff" />
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
47 <output name="output_genes_csv_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv" />
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
48 <output name="output_gw_png_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png" />
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
49 </test>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
50 </tests>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
51 <help>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
52 .. class:: warningmark
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
53
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
54
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
55 Check the documentation for setting the tool parameters at the source code repository: http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
56
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
57 -----
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
58
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
59 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
60 :height: 80
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
61 :width: 200
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
62
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
63 **http://mmb.irbbarcelona.org/NucleosomeDynamics**
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
64 </help>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
65 <citations>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
66 <citation type="bibtex">
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
67 @misc{github,
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
68 author = {Buitrago D},
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
69 year = {2019},
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
70 title = {Nucleosome Dynamics suite: containerized installation},
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
71 publisher = {GitLab},
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
72 journal = {GitLab repository},
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
73 url = {http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker},
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
74 }</citation>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
75 </citations>
|
spanish_national_institue_of_bioinformatics
parents:
diff
changeset
|
76 </tool>
|
