Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison readmap.xml @ 1:eee9701a7491 draft

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author mvdbeek
date Sun, 29 Mar 2015 13:07:57 -0400
parents 9af9983dcd02
children 4895f7c6ae4d
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0:9af9983dcd02 1:eee9701a7491
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 6 <requirement type="package" version="0.7.7">pysam</requirement>
7 <requirement type="package" version="2.14">biocbasics</requirement> 7 <requirement type="package" version="2.14">biocbasics</requirement>
8 <requirement type="package" version="3.0.3">R</requirement> 8 <requirement type="package" version="3.0.3">R</requirement>
9 <requirement type="package" version="1.9">numpy</requirement>
10 <requirement type="package" version="0.14">scipy</requirement>
9 </requirements> 11 </requirements>
10 <parallelism method="basic"></parallelism>
11 <command interpreter="python"> 12 <command interpreter="python">
12 readmap.py 13 readmap.py
13 #if $refGenomeSource.genomeSource == "history": 14 #if $refGenomeSource.genomeSource == "history":
14 --reference_fasta ## sys.argv[2] 15 --reference_fasta ## sys.argv[2]
15 $refGenomeSource.ownFile ## index source 16 $refGenomeSource.ownFile ## index source
256 .. image:: static/images/readmap.png 257 .. image:: static/images/readmap.png
257 :height: 800 258 :height: 800
258 :width: 500 259 :width: 500
259 260
260 </help> 261 </help>
261 262 <tests>
262 <test> 263 <test>
263 <param name="genomeSource" value="history" /> 264 <param name="genomeSource" value="history" />
264 <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> 265 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
265 <param name="input" value="sample1.srbowtie_out, sample2.srbowtie_out, sample3.srbowtie_out" ftype="tabular" /> 266 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
266 <param name="norm" value="1,1,1" /> 267 <param name="series_0|norm" value="1" />
268 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
269 <param name="series_1|norm" value="1" />
270 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
271 <param name="series_2|norm" value="1" />
267 <param name="minquery" value="20" /> 272 <param name="minquery" value="20" />
268 <param name="maxquery" value="30" /> 273 <param name="maxquery" value="30" />
269 <param name="title" value="Readmaps and size distributions" /> 274 <param name="title" value="Readmaps and size distributions" />
270 <param name="xlabel" value="Coordinates/read size" /> 275 <param name="xlabel" value="Coordinates/read size" />
271 <param name="ylabel" value="Number of reads" /> 276 <param name="ylabel" value="Number of reads" />
272 <param name="rows_per_page" value="8" /> 277 <param name="rows_per_page" value="8" />
273 <output name="readmap_dataframe" ftype="tabular" value="Readmap_dataframe.tab" /> 278 <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" />
274 <output name="size_distribution_dataframe" ftype="tabular" value="Size_distribution_dataframe.tab" /> 279 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
275 <output name="readmap_PDF" ftype="pdf" value="Readmaps.pdf" /> 280 <output name="readmap_PDF" ftype="pdf" file="Readmaps.pdf" />
276 <output name="size_PDF" ftype="pdf" value="Size_distribution.pdf" /> 281 <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
277 <output name="combi_PDF" ftype="pdf" value="Size_distribution_and_Readmaps.pdf" /> 282 <output name="combi_PDF" ftype="pdf" file="Size_distribution_and_Readmaps.pdf" />
278 </test> 283 </test>
279 284 </tests>
280 </tool> 285 </tool>