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