Mercurial > repos > mvdbeek > bam_readtagger
comparison plot_coverage.xml @ 78:6178c24ddd5a draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
| author | mvdbeek |
|---|---|
| date | Tue, 07 Apr 2020 08:57:47 -0400 |
| parents | b9b76f9a816c |
| children | c42dd2551c9c |
comparison
equal
deleted
inserted
replaced
| 77:b9b76f9a816c | 78:6178c24ddd5a |
|---|---|
| 1 <tool id="plot_coverage" name="Plot coverage" version="0.5.23"> | 1 <tool id="plot_coverage" name="Plot coverage" version="0.5.24"> |
| 2 <description>as area plot between BAM files</description> | 2 <description>as area plot between BAM files</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.5.23">readtagger</requirement> | 4 <requirement type="package" version="0.5.24">readtagger</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="aggressive"><![CDATA[ | 6 <command detect_errors="aggressive"><![CDATA[ |
| 7 #import re | 7 #import re |
| 8 plot_coverage | 8 plot_coverage |
| 9 #for $r in $input_files | 9 #for $r in $input_files |
| 10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier)) | 10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier)) |
| 11 --file '$r.input' '$identifier' $r.total_reads | 11 --file '$r.input' '$identifier' $r.total_reads |
| 12 #end for | 12 #end for |
| 13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' | 13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind |
| 14 ]]></command> | 14 ]]></command> |
| 15 <inputs> | 15 <inputs> |
| 16 <repeat name="input_files" title="Add input files to coverage plot" min="1"> | 16 <repeat name="input_files" title="Add input files to coverage plot" min="1"> |
| 17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/> | 17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/> |
| 18 <param name="total_reads" type="integer" value="0" min="0" label="Total number of (mapped) reads. If given plot scale will be reads per million"/> | 18 <param name="total_reads" type="integer" value="0" min="0" label="Total number of (mapped) reads. If given plot scale will be reads per million"/> |
| 25 <add value=":" /> | 25 <add value=":" /> |
| 26 <add value="." /> | 26 <add value="." /> |
| 27 </valid> | 27 </valid> |
| 28 </sanitizer> | 28 </sanitizer> |
| 29 </param> | 29 </param> |
| 30 <param name="plot_kind" type="select" label="Select the plot type"> | |
| 31 <option value="area">Area plot</option> | |
| 32 <option value="line">Line plot</option> | |
| 33 </param> | |
| 30 </inputs> | 34 </inputs> |
| 31 <outputs> | 35 <outputs> |
| 32 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> | 36 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> |
| 33 </outputs> | 37 </outputs> |
| 34 <tests> | 38 <tests> |
| 38 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/> | 42 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/> |
| 39 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/> | 43 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/> |
| 40 <param name="regions" value="3R:13373525-13373615"/> | 44 <param name="regions" value="3R:13373525-13373615"/> |
| 41 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> | 45 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> |
| 42 </test> | 46 </test> |
| 47 <test> | |
| 48 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/> | |
| 49 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/> | |
| 50 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/> | |
| 51 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/> | |
| 52 <param name="regions" value="3R:13373525-13373615"/> | |
| 53 <param name="plot_kind" value="line"/> | |
| 54 <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/> | |
| 55 </test> | |
| 43 </tests> | 56 </tests> |
| 44 <help><![CDATA[ | 57 <help><![CDATA[ |
| 45 | 58 |
| 46 This tool plots the coverage over a specified region (by default all chromosomes/contigs). | 59 This tool plots the coverage over a specified region (by default all chromosomes/contigs). |
| 47 | 60 |