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comparison cummeRbund.xml @ 5:78fcfc04fcfe draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3
author devteam
date Thu, 23 Feb 2017 20:24:03 -0500
parents ba8fde59843d
children c3b54a4b7741
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4:ba8fde59843d 5:78fcfc04fcfe
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="cummeRbund" name="cummeRbund" version="1.0.1"> 2 <tool id="cummeRbund" name="cummeRbund" version="2.16.0">
3 <description>visualize Cuffdiff output</description> 3 <description>visualize Cuffdiff output</description>
4 <requirements>
5 <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>
6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="package" version="2.8.2">cummeRbund</requirement>
8 </requirements>
9 <expand macro="stdio" />
10 <macros> 4 <macros>
11 <import>cummeRbund_macros.xml</import> 5 <import>cummeRbund_macros.xml</import>
12 </macros> 6 </macros>
7 <requirements>
8 <requirement type="package" version="1.0.1">r-argparse</requirement>
9 <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
10 </requirements>
13 <code file="cummeRbund_options.py"/> 11 <code file="cummeRbund_options.py"/>
14 <command> 12 <command detect_errors="aggressive">
15 <![CDATA[ 13 <![CDATA[
16 #for i, p in enumerate($plots): 14 #for i, p in enumerate($plots):
17 R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args 15 Rscript $__tool_directory__/cummeRbund.R
18 --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}" 16 --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"
19 --outfile plot-${p.plot.type}-${i}.png 17 --outfile plot-${p.plot.type}-${i}.png
20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]: 18 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
21 $p.plot.replicates 19 $p.plot.replicates
22 #elif $p.plot.type == "scatter": 20 #elif $p.plot.type == "scatter":
38 #end for 36 #end for
39 #end if 37 #end if
40 #elif $p.plot.type == "heatmap": 38 #elif $p.plot.type == "heatmap":
41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10 39 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
42 #if len($p.plot.genes) > 0: 40 #if len($p.plot.genes) > 0:
41 --gene_selector
43 #for gene in $p.plot.genes: 42 #for gene in $p.plot.genes:
44 --genes ${gene.gene_id} 43 --genes ${gene.gene_id}
45 #end for 44 #end for
46 #end if 45 #end if
47 #elif $p.plot.type == "cluster": 46 #elif $p.plot.type == "cluster":
122 <option value="column">Column</option> 121 <option value="column">Column</option>
123 <option value="both" selected="true">Both</option> 122 <option value="both" selected="true">Both</option>
124 <option value="none">None</option> 123 <option value="none">None</option>
125 </param> 124 </param>
126 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/> 125 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
127 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/> 126 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display row labels?"/>
128 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/> 127 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
129 <expand macro="log10_checkbox" /> 128 <expand macro="log10_checkbox" />
130 </when> 129 </when>
131 <when value="cluster"> 130 <when value="cluster">
132 <expand macro="features_selector" /> 131 <expand macro="features_selector" />
270 <param name="width" value="1280" /> 269 <param name="width" value="1280" />
271 <param name="height" value="960" /> 270 <param name="height" value="960" />
272 <conditional name="plot"> 271 <conditional name="plot">
273 <param name="type" value="heatmap" /> 272 <param name="type" value="heatmap" />
274 <repeat name="genes"> 273 <repeat name="genes">
275 <param name="gene_id" value="XLOC_000078" /> 274 <param name="gene_id" value="XLOC_000030" />
275 </repeat>
276 <repeat name="genes">
277 <param name="gene_id" value="XLOC_000037" />
276 </repeat> 278 </repeat>
277 </conditional> 279 </conditional>
278 </repeat> 280 </repeat>
279 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2"> 281 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
280 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" /> 282 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
351 <help><![CDATA[ 353 <help><![CDATA[
352 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. 354 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
353 355
354 ------ 356 ------
355 357
356 Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute. 358 Based on the `cummeRbund wrapper <https://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
357 ]]></help> 359 ]]></help>
358 <citations> 360 <citations>
359 <citation type="doi">doi:10.1038/nprot.2012.016</citation> 361 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
360 </citations> 362 </citations>
361 </tool> 363 </tool>