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comparison stiffness_stats.xml @ 2:e88c806ddf3e draft default tip

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author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 05:28:43 -0400
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1:707216744193 2:e88c806ddf3e
1 <tool id="stiffness_stats" name="Stiffness Statistics" version="0.1">
2 <description>: gather gene and genome-wide statistics on nucleosome position stiffness</description>
3 <requirements>
4 <requirement type="binary">docker</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 ln -f -s $output_gw2_png_file $output_gw2_png_file\.png;
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 stiffness_stats --input $gff_file
10 #if $assembly.source == "buildin":
11 --genome ${assembly.ref_genome_gff_buildin}
12 #else if $assembly.source == "history":
13 --genome ${assembly.ref_genome_gff_history}
14 #end if
15 --out_genes $output_genes_csv_file --out_gw $output_gw_csv_file --out_gw2 $output_gw2_png_file\.png;
16 rm $output_gw2_png_file\.png
17 ]]>
18 </command>
19 <inputs>
20 <param name="gff_file" type="data" format="gff" label="Stiffness (GFF)" help="Stiffness as annotated by Stiffness tool." />
21 <conditional name="assembly">
22 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
23 <option value="buildin" selected="True">Use a built-in genome</option>
24 <option value="history">Use a genome from the history</option>
25 </param>
26 <when value="buildin">
27 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
28 <options from_file="nucldyn_publicdata.loc">
29 <column name="name" index="2"/>
30 <column name="value" index="4"/>
31 </options>
32 </param>
33 </when>
34 <when value="history">
35 <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <data format="csv" name="output_genes_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
41 <data format="csv" name="output_gw_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" />
42 <data format="png" name="output_gw2_png_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw2.png" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="gff_file" value="STF__cellcycleM_chrII.gff" />
47 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
48 <output name="output_genes_csv_file" file="STF__stats__cellcycleM_chrII.genes.csv" />
49 <output name="output_gw_csv_file" file="STF__stats__cellcycleM_chrII.gw.csv" />
50 <output name="output_gw2_png_file" file="STF__stats__cellcycleM_chrII.gw2.png" />
51 </test>
52 </tests>
53 <help>
54 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
55 :height: 80
56 :width: 200
57
58 -----
59
60 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.
61
62 .. class:: infomark
63
64 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
65 </help>
66 <citations>
67 <citation type="bibtex">
68 @misc{github,
69 author = {Buitrago D},
70 year = {2019},
71 title = {Nucleosome Dynamics suite: containerized installation},
72 publisher = {GitHub},
73 journal = {GitHub repository},
74 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
75 }</citation>
76 </citations>
77 </tool>