Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

annotate 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 <tool id="txstart_stats" name="TSS Statistics" version="0.1">
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2 <description>: gather gene and genome-wide statistics on nucleosomes at TSS</description>
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3 <requirements>
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4 <requirement type="binary">docker</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 ln -f -s $output_gw_png_file $output_gw_png_file\.png;
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9 ln -f -s $output_gw2_png_file $output_gw2_png_file\.png;
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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
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11 #if $assembly.source == "buildin":
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12 --genome ${assembly.ref_genome_gff_buildin}
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13 #else if $assembly.source == "history":
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14 --genome ${assembly.ref_genome_gff_history}
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15 #end if
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16 --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png --out_gw2 $output_gw2_png_file\.png;
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17 rm $output_gw_png_file\.png;
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18 rm $output_gw2_png_file\.png
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Transcription Start Sites as annotated by TSS classification tool."/>
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23 <conditional name="assembly">
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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.">
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25 <option value="buildin" selected="True">Use a built-in genome</option>
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26 <option value="history">Use a genome from the history</option>
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27 </param>
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28 <when value="buildin">
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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.">
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30 <options from_file="nucldyn_publicdata.loc">
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31 <column name="name" index="2"/>
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32 <column name="value" index="4"/>
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33 </options>
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34 </param>
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35 </when>
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36 <when value="history">
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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."/>
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data format="csv" name="output_genes_csv_file" label="TSS__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
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43 <data format="png" name="output_gw_png_file" label="TSS__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" />
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44 <data format="png" name="output_gw2_png_file" label="TSS__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw2.png" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="gff_file" value="TSS__cellcycleM_chrII.gff" />
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49 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
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50 <output name="output_genes_csv_file" file="TSS__stats__cellcycleM_chrII.genes.csv" />
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51 <output name="output_gw_png_file" file="TSS__stats__cellcycleM_chrII.gw.png" />
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52 <output name="output_gw2_png_file" file="TSS__stats__cellcycleM_chrII.gw2.png" />
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53 </test>
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54 </tests>
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55 <help>
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56 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
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57 :height: 80
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58 :width: 200
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59
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60 -----
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61
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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.
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63
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64 .. class:: infomark
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65
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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
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67 </help>
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68 <citations>
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69 <citation type="bibtex">
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70 @misc{github,
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71 author = {Buitrago D},
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72 year = {2019},
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73 title = {Nucleosome Dynamics suite: containerized installation},
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74 publisher = {GitHub},
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75 journal = {GitHub repository},
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76 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
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77 }</citation>
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78 </citations>
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79 </tool>