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comparison bamedit.xml @ 44:80871d2d80a4 draft

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Uploaded
author zzhou
date Mon, 26 Nov 2012 13:37:36 -0500
parents 3de9eff1d0b7
children abdad2099043
comparison
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43:6c4c96895ae7 44:80871d2d80a4
3 author: Ziru Zhou 3 author: Ziru Zhou
4 date: October, 2012 4 date: October, 2012
5 --> 5 -->
6 <tool id="BAM_Editor" name="BAMEdit" version="1.1.0"> 6 <tool id="BAM_Editor" name="BAMEdit" version="1.1.0">
7 <requirements> 7 <requirements>
8 <requirement type="set_enviornment">SCRIPT_PATH</requirement>
8 <requirement type="package" version="0.1.12">samtools</requirement> 9 <requirement type="package" version="0.1.12">samtools</requirement>
9 </requirements> 10 </requirements>
10 <description>Merging, splitting, filtering, and QC of BAM files</description> 11 <description>Merging, splitting, filtering, and QC of BAM files</description>
11 <command interpreter="python">bamedit.py $options_file</command> 12 <command interpreter="python">bamedit.py $options_file $SCRIPT_PATH</command>
12 <inputs> 13 <inputs>
13 <conditional name="input_type"> 14 <conditional name="input_type">
14 <param name="input_type_selector" type="select" label="Select your BAM command"> 15 <param name="input_type_selector" type="select" label="Select your BAM command">
15 <option value="merge">Merge BAM files</option> 16 <option value="merge">Merge BAM files</option>
16 <option value="split">Split BAM file</option> 17 <option value="split">Split BAM file</option>
71 #else: 72 #else:
72 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) } 73 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) }
73 #end if 74 #end if
74 #end if 75 #end if
75 #if str($input_type.input_type_selector) == 'split': 76 #if str($input_type.input_type_selector) == 'split':
76 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1), 'spath':str(\$SCRIPT_PATH) } 77 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
77 #end if 78 #end if
78 #if str($input_type.input_type_selector) == 'filter': 79 #if str($input_type.input_type_selector) == 'filter':
79 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) } 80 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }
80 #end if 81 #end if
81 #if str($input_type.input_type_selector) == 'pileup': 82 #if str($input_type.input_type_selector) == 'pileup':