Mercurial > repos > drosofff > msp_sr_size_histograms

comparison size_histogram.xml @ 1:6c72cf9a00df draft

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author mvdbeek
date Sun, 29 Mar 2015 12:54:10 -0400
parents 63ff807752d7
children 9f75d887904d
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0:63ff807752d7 1:6c72cf9a00df
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 size_histogram.py 13 size_histogram.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
213 .. image:: static/images/size_histogram.png 214 .. image:: static/images/size_histogram.png
214 :height: 800 215 :height: 800
215 :width: 500 216 :width: 500
216 217
217 </help> 218 </help>
219 <tests>
218 <test> 220 <test>
219 <param name="genomeSource" value="history" /> 221 <param name="genomeSource" value="history" />
220 <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> 222 <param name="ownFile" value="transposons.fasta" ftype="fasta" />
221 <param name="input" value="sample1.srbowtie_out, sample2.srbowtie_out, sample3.srbowtie_out" ftype="tabular" /> 223 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
222 <param name="norm" value="1,1,1" /> 224 <param name="series_0|norm" value="1" />
225 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
226 <param name="series_1|norm" value="1" />
227 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
228 <param name="series_2|norm" value="1" />
223 <param name="global" value="no" /> 229 <param name="global" value="no" />
224 <param name="collapsestrands" value="no" /> 230 <param name="collapsestrands" value="no" />
225 <param name="minquery" value="18"/> 231 <param name="minquery" value="18"/>
226 <param name="maxquery" value="30"/> 232 <param name="maxquery" value="30"/>
227 <param name="title" value="Size distribution"/> 233 <param name="title" value="Size distribution"/>
228 <param name="xlabel" value="Size in nucleotides"/> 234 <param name="xlabel" value="Size in nucleotides"/>
229 <param name="ylabel" value="Number of reads"/> 235 <param name="ylabel" value="Number of reads"/>
230 <param name="rows_per_page" value="10"/> 236 <param name="rows_per_page" value="10"/>
231 <output name="size_distribution_dataframe" ftype="tabular" value="Size_distribution_dataframe.tab" /> 237 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
232 <output name="size_PDF" ftype="pdf" value="Size_distribution.pdf" /> 238 <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
233 </test> 239 </test>
240 </tests>
234 </tool> 241 </tool>
235 242