nucleosome_dynamics: stiffness

annotate stiffness_stats.xml @ 2:e88c806ddf3e draft default tip

Uploaded

author	spanish_national_institue_of_bioinformatics
date	Fri, 12 Apr 2019 05:28:43 -0400
parents
children

rev	line source
2 e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	1 <tool id="stiffness_stats" name="Stiffness Statistics" version="0.1">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: gather gene and genome-wide statistics on nucleosome position stiffness</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_gw2_png_file $output_gw2_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 stiffness_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_csv_file --out_gw2 $output_gw2_png_file\.png;
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 rm $output_gw2_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="Stiffness (GFF)" help="Stiffness as annotated by Stiffness tool." />
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="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 <data format="csv" name="output_gw_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 <data format="png" name="output_gw2_png_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw2.png" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 </outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	44 <tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 <test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 <param name="gff_file" value="STF__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 <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	48 <output name="output_genes_csv_file" file="STF__stats__cellcycleM_chrII.genes.csv" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 <output name="output_gw_csv_file" file="STF__stats__cellcycleM_chrII.gw.csv" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	50 <output name="output_gw2_png_file" file="STF__stats__cellcycleM_chrII.gw2.png" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	51 </test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	52 </tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	53 <help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	54 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	55 :height: 80
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	56 :width: 200
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	57
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	58 -----
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	59
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	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.
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	61
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	62 .. class:: infomark
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	63
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	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
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	65 </help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	66 <citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	67 <citation type="bibtex">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	68 @misc{github,
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	69 author = {Buitrago D},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	70 year = {2019},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	71 title = {Nucleosome Dynamics suite: containerized installation},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	72 publisher = {GitHub},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	73 journal = {GitHub repository},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	74 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	75 }</citation>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	76 </citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	77 </tool>

Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

annotate stiffness_stats.xml @ 2:e88c806ddf3e draft default tip