Mercurial > repos > bgruening > bismark

comparison bismark_methylation_extractor.xml @ 3:91f07ff056ca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 14 Apr 2014 16:43:14 -0400
parents 62c6da72dd4a
children 243e8f9fb75b
comparison
equal deleted inserted replaced
2:82814a8a2395 3:91f07ff056ca
1 <tool id="bismark_methylation_extractor" name="Bismark" version="0.7.12"> 1 <tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.1">
2 <!-- Wrapper compatible with Bismark version 0.7.7 --> 2 <!-- Wrapper compatible with Bismark version 0.10 -->
3 <description>methylation extractor</description> 3 <description>Reports on methylation status of reads mapped by Bismark</description>
4 <!--<version_command>bismark_methylation_extractor version</version_command>--> 4 <!--<version_command>bismark_methylation_extractor version</version_command>-->
5 <requirements> 5 <requirements>
6 <requirement type="set_environment">SCRIPT_PATH</requirement> 6 <requirement type="set_environment">SCRIPT_PATH</requirement>
7 <requirement type="package" version="0.12.8">bowtie</requirement> 7 <requirement type="package" version="0.12.8">bowtie</requirement>
8 <requirement type="package" version="2.0.0-beta7">bowtie2</requirement> 8 <requirement type="package" version="2.1.0">bowtie2</requirement>
9 </requirements> 9 </requirements>
10 <parallelism method="basic"></parallelism> 10 <parallelism method="basic"></parallelism>
11 <command interpreter="python"> 11 <command interpreter="python">
12 bismark_methylation_extractor.py 12 bismark_methylation_extractor.py
13 13
79 #end if 79 #end if
80 80
81 </command> 81 </command>
82 <inputs> 82 <inputs>
83 <!-- Input Parameters --> 83 <!-- Input Parameters -->
84 <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" /> 84 <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" />
85 <conditional name="singlePaired"> 85 <conditional name="singlePaired">
86 <param name="sPaired" type="select" label="Is this library mate-paired?"> 86 <param name="sPaired" type="select" label="Is this library mate-paired?">
87 <option value="single">Single-end</option> 87 <option value="single">Single-end</option>
88 <option value="paired">Paired-end</option> 88 <option value="paired">Paired-end</option>
89 </param> 89 </param>
90 <when value="single" /> 90 <when value="single" />
91 <when value="paired"> 91 <when value="paired">
92 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" /> 92 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" />
93 </when> 93 </when>
94 </conditional> 94 </conditional>
95
96 <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" /> 95 <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" />
97 <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info 96 <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info
98 into context-dependent output files" help="" /> 97 into context-dependent output files" help="" />
99 <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." /> 98 <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." />
100 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" /> 99 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" />