Mercurial > repos > mvdbeek > mismatch_frequencies

comparison mismatch_frequencies.xml @ 3:edae148b2dd4

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Add tool-test.
author mvdbeek
date Tue, 27 Jan 2015 17:44:42 +0100
parents 1609cb745999
children dd09eada7b78
comparison
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2:2417a9361d1a 3:edae148b2dd4
1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.3" hidden="false" > 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.3" hidden="false" >
2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description> 2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.7">pysam</requirement> 4 <requirement type="package" version="0.7.7">pysam</requirement>
5 <requirement type="package" version="0.14">pandas</requirement> 5 <requirement type="package" version="0.14">pandas</requirement>
6 <requirement type="package" version="1.4">matplotlib</requirement> 6 <requirement type="package" version="1.4">matplotlib</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python">mismatch_frequencies.py --input 8 <command interpreter="python">mismatch_frequencies.py --input
9 #for i in $rep 9 #for i in $rep
10 "$i.input_file" 10 "$i.input_file"
11 #end for 11 #end for
12 --name 12 --name
13 #for i in $rep 13 #for i in $rep
15 #end for 15 #end for
16 --output_pdf $output_pdf --output_tab $output_tab --min $min_length --max $max_length 16 --output_pdf $output_pdf --output_tab $output_tab --min $min_length --max $max_length
17 --n_mm $number_of_mismatches 17 --n_mm $number_of_mismatches
18 --five_p $five_p 18 --five_p $five_p
19 --three_p $three_p 19 --three_p $three_p
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <repeat name="rep" title="alignment files"> 22 <repeat name="rep" title="alignment files">
23 <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/> 23 <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/>
24 </repeat> 24 </repeat>
25 <param name="number_of_mismatches" label="Maximum number of allowed mismatches per read" help="Discard reads with more than the chosen number of mismatches from the frequency calculation" type="integer" value="3"/> 25 <param name="number_of_mismatches" label="Maximum number of allowed mismatches per read" help="Discard reads with more than the chosen number of mismatches from the frequency calculation" type="integer" value="3"/>
26 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/> 26 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/>
27 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/> 27 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/>
28 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/> 28 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/>
29 <param name="three_p" label="Ignore mismatches in the last N nucleotides of a read" help="useful to discriminate between tailing events and editing events" type="integer" value="3"/> 29 <param name="three_p" label="Ignore mismatches in the last N nucleotides of a read" help="useful to discriminate between tailing events and editing events" type="integer" value="3"/>
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data format="pdf" name="output_pdf" /> 32 <data format="tabular" name="output_tab" />
33 <data format="tabular" name="output_tab" /> 33 <data format="pdf" name="output_pdf" />
34 </outputs> 34 </outputs>
35 35 <tests>
36 <test>
37 <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
38 <param name="rep_1|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
39 <param name="number_of_mismatches" value="1" />
40 <param name="min_length" value="21" />
41 <param name="max_length" value="21" />
42 <output name="tabular" file="mismatch.tab" ftype="tabular"/>
43 <output name="pdf" file="mismatch.pdf" ftype="pdf"/>
44 </test>
45 </tests>
36 </tool> 46 </tool>