Mercurial > repos > mvdbeek > mismatch_frequencies

comparison mismatch_frequencies.xml @ 19:f7da7f3e2c98

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Sun, 24 May 2015 11:12:24 -0400
parents e3d950e52e38
children 11a1dae1ab8e
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18:e3d950e52e38 19:f7da7f3e2c98
1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.7" hidden="false" > 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.8" 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="0.14.1">pandas</requirement> 5 <requirement type="package" version="0.14.1">pandas</requirement>
6 <requirement type="package" version="1.2.1">matplotlib</requirement> 6 <requirement type="package" version="1.2.1">matplotlib</requirement>
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 --expanded_output_tab $expanded_tab
21 --possible_mismatches $possible_mismatches
20 </command> 22 </command>
21 <inputs> 23 <inputs>
22 <repeat name="rep" title="alignment files"> 24 <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."/> 25 <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> 26 </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"/> 27 <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"/>
28 <param name="possible_mismatches" label="Specify mismatches that should be counted" help="Ignores mismatches that are not listed" type="text" value="AC AG AT CA CG CT GA GC GT TA TC TG">
29 <validator type="expression" message="Allowed values are AGCTN, seperated by space.">len([False for char in value if not char in " AGCTN"]) == 0</validator>
30 </param>
26 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/> 31 <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"/> 32 <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"/> 33 <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"/> 34 <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"/>
35 <param help="Output expanded tabular format" label="Nucleotide mismatches per reference sequence" name="expanded" type="select">
36 <option select="true" value="false">No</option>
37 <option value="expanded">Yes</option>
38 </param>
30 </inputs> 39 </inputs>
31 <outputs> 40 <outputs>
32 <data format="tabular" name="output_tab" /> 41 <data format="tabular" name="output_tab" />
42 <data format="fasta" name="expanded_tab">
43 <filter> expanded == "expanded"</filter>
44 </data>
33 <data format="pdf" name="output_pdf" /> 45 <data format="pdf" name="output_pdf" />
34 </outputs> 46 </outputs>
35 <tests> 47 <tests>
36 <test> 48 <test>
37 <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" /> 49 <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
70 This tool skips all read that have insertions and has been tested only with bowtie and bowtie2 82 This tool skips all read that have insertions and has been tested only with bowtie and bowtie2
71 generated alignment files. 83 generated alignment files.
72 84
73 Written by Marius van den Beek, m.vandenbeek at gmail . com 85 Written by Marius van den Beek, m.vandenbeek at gmail . com
74 </help> 86 </help>
87 <citations>
88 </citations>
75 </tool> 89 </tool>