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comparison samtool_filter2.xml @ 13:aa8dc5cf70be draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828
author devteam
date Thu, 17 Mar 2016 11:41:18 -0400
parents 543405859e60
children cc2b231ab5e1
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12:543405859e60 13:aa8dc5cf70be
1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.1"> 1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">
2 <description>files on FLAG MAPQ RG LN or by region</description> 2 <description>files on FLAG MAPQ RG LN or by region</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.18">samtools</requirement> 4 <requirement type="package" version="1.2">samtools</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
15 ln -s "$input1.metadata.bam_index" input.bai && 15 ln -s "$input1.metadata.bam_index" input.bai &&
16 #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__): 16 #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__):
17 #set $input = 'input.sam' 17 #set $input = 'input.sam'
18 ln -s "$input1" $input && 18 ln -s "$input1" $input &&
19 #end if 19 #end if
20 samtools view -o "$output1" $header 20 samtools view $possibly_select_inverse "$output1" $header
21 21
22 #if $input1.datatype.file_ext == 'sam': 22 #if $input1.datatype.file_ext == 'sam':
23 -S 23 -S
24 #end if 24 #end if
25 25
113 <param name="library" type="text" value="" label="Select alignments from Library" 113 <param name="library" type="text" value="" label="Select alignments from Library"
114 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> 114 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
115 <param name="read_group" type="text" value="" label="Select alignments from Read Group" 115 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
116 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> 116 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
117 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/> 117 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
118 <param name="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" />
118 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)" 119 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
119 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/> 120 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
120 <param name="outputtype" type="select" label="Select the output format"> 121 <param name="outputtype" type="select" label="Select the output format">
121 <option value="bam">BAM (-b)</option> 122 <option value="bam">BAM (-b)</option>
122 <option value="sam">SAM</option> 123 <option value="sam">SAM</option>