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comparison bamedit.xml @ 62:4ebe0aa42cf0 draft

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author zzhou
date Mon, 26 Nov 2012 14:27:02 -0500
parents 22ad413dd345
children fdad5f2a7ad9
comparison
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61:ad92d59fb5e2 62:4ebe0aa42cf0
7 <requirements> 7 <requirements>
8 <requirement type="set_enviornment">SCRIPT_PATH</requirement> 8 <requirement type="set_enviornment">SCRIPT_PATH</requirement>
9 <requirement type="package" version="0.1.12">samtools</requirement> 9 <requirement type="package" version="0.1.12">samtools</requirement>
10 </requirements> 10 </requirements>
11 <description>Merging, splitting, filtering, and QC of BAM files</description> 11 <description>Merging, splitting, filtering, and QC of BAM files</description>
12 <command interpreter="python">bamedit.py $options_file str(\$SCRIPT_PATH)</command> 12 <command interpreter="python">bamedit.py $options_file '\SCRIPT_PATH'</command>
13 <inputs> 13 <inputs>
14 <conditional name="input_type"> 14 <conditional name="input_type">
15 <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">
16 <option value="merge">Merge BAM files</option> 16 <option value="merge">Merge BAM files</option>
17 <option value="split">Split BAM file</option> 17 <option value="split">Split BAM file</option>
72 #else: 72 #else:
73 #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) }
74 #end if 74 #end if
75 #end if 75 #end if
76 #if str($input_type.input_type_selector) == 'split': 76 #if str($input_type.input_type_selector) == 'split':
77 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) } 77 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1), 'testing':str('\$SCRIPT_PATH') }
78 #end if 78 #end if
79 #if str($input_type.input_type_selector) == 'filter': 79 #if str($input_type.input_type_selector) == 'filter':
80 #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) }
81 #end if 81 #end if
82 #if str($input_type.input_type_selector) == 'pileup': 82 #if str($input_type.input_type_selector) == 'pileup':